From 84267cf2139b8255c9a0d5c7e502b4ff77709e21 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Wed, 24 May 2023 09:04:06 -0700 Subject: [PATCH] Add pipeline for fetching and transforming submission portal entry (#247) * Add stub Dagster resource for accessing submission portal data API This is just pulling from a hardcoded sample file until the data API's authentication scheme is worked out * Add Dagster op to wrap data API call to get metadata * Add Translator subclass for submission portal metadata Currently this includes logic to generate a Study object. Translating Biosample objects still to do. * Use shared fake ID minting test fixture in translator tests * Add translation of biosamples to SubmissionPortalTranslator * Add tests for SubmissionPortalTranslator helper methods * Add integration test case for submission portal translator * Handle multivalued slots * Add graph and job for submission portal metadata transformation * Add ops for metadata submission and run status polling * Split portal ingest graph into dry run and actual submit graphs * Clean up empty strings and lists in submission portal translator * Add docstrings for submission portal translator * Update submission metadata graph names and add job descriptions * Add validation step to submission ingest dry run job * Get portal session cookie from launch config instead of environment * Add smoke test for submission data translation job * fix: hash checking is problematic * regen reqs * remove mongo dep from test container * feat: no need for mongo in `test` image * resolve * finish merge * Remove fields that should be null from submission portal translator expected output * Pass submission id through op config in test * style: black autofmt * feat: better startup invocation * Remove unnecessary raise_for_status calls * fix: double type recognized * test double-type fix * style: refactor mgmt stuff --------- Co-authored-by: Donny Winston --- .env.example | 2 + docker-compose.test.yml | 2 +- docker-compose.yml | 2 +- nmdc_runtime/api/core/metadata.py | 7 +- nmdc_runtime/api/endpoints/runs.py | 24 +- nmdc_runtime/api/main.py | 116 +- nmdc_runtime/api/models/run.py | 20 +- nmdc_runtime/site/graphs.py | 26 + nmdc_runtime/site/ops.py | 90 +- nmdc_runtime/site/repository.py | 96 +- nmdc_runtime/site/resources.py | 130 +- .../site/translation/gold_translator.py | 17 +- .../submission_portal_translator.py | 442 + nmdc_runtime/site/translation/translator.py | 22 + setup.py | 10 - tests/files/nmdc:bsm-11-5nhz3402.json | 66 + .../files/test_changesheet_update_one_ph.tsv | 2 + tests/test_api/test_metadata.py | 19 + tests/test_data/conftest.py | 19 + tests/test_data/test_gold_translator.py | 16 +- .../test_submission_portal_translator.py | 252 + ...est_submission_portal_translator_data.yaml | 13203 ++++++++++++++++ .../test_submission_portal_graphs.py | 130 + tests/test_ops/test_data_api_ops.py | 36 + util/mongodump-nmdc.sh | 12 +- util/mongorestore-nmdc.sh | 5 +- 26 files changed, 14593 insertions(+), 173 deletions(-) create mode 100644 nmdc_runtime/site/translation/submission_portal_translator.py create mode 100644 nmdc_runtime/site/translation/translator.py create mode 100644 tests/files/nmdc:bsm-11-5nhz3402.json create mode 100644 tests/files/test_changesheet_update_one_ph.tsv create mode 100644 tests/test_data/conftest.py create mode 100644 tests/test_data/test_submission_portal_translator.py create mode 100644 tests/test_data/test_submission_portal_translator_data.yaml create mode 100644 tests/test_graphs/test_submission_portal_graphs.py create mode 100644 tests/test_ops/test_data_api_ops.py diff --git a/.env.example b/.env.example index 48c3696d..24b99c3f 100644 --- a/.env.example +++ b/.env.example @@ -30,3 +30,5 @@ DAGIT_HOST=http://dagster-dagit:3000 GOLD_API_BASE_URL=https://gold.jgi.doe.gov/rest/nmdc GOLD_API_USERNAME=x GOLD_API_PASSWORD=x + +NMDC_PORTAL_API_BASE_URL=https://data-dev.microbiomedata.org/ diff --git a/docker-compose.test.yml b/docker-compose.test.yml index 602a5475..04305fca 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -82,7 +82,7 @@ services: - nmdc_runtime_mongo_data:/data/db - ~/nmdcdb-mongodump:/nmdc_dump:ro - ./tests/mongorestore-nmdc-testdb.sh:/mongorestore-nmdc-testdb.sh:ro - restart: always + restart: unless-stopped environment: MONGODB_ROOT_USER: admin MONGODB_ROOT_PASSWORD: root diff --git a/docker-compose.yml b/docker-compose.yml index ce65b098..f31970a4 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -82,7 +82,7 @@ services: volumes: - nmdc_runtime_mongo_data:/data/db - ./tests:/app_tests - restart: always + restart: unless-stopped environment: MONGODB_ROOT_USER: admin MONGODB_ROOT_PASSWORD: root diff --git a/nmdc_runtime/api/core/metadata.py b/nmdc_runtime/api/core/metadata.py index 55844c0f..f106000e 100644 --- a/nmdc_runtime/api/core/metadata.py +++ b/nmdc_runtime/api/core/metadata.py @@ -213,7 +213,12 @@ def load_changesheet( for ix, value, ranges in list(df[["value", "ranges"]].itertuples()): # TODO make this way more robust, # i.e. detect a range with a https://w3id.org/linkml/base of "float". - if ranges.endswith("float") or ranges.endswith("decimal degree"): + # TODO mongo BSON has a decimal type. Should use this for decimals! + if ( + ranges.endswith("float") + or ranges.endswith("double") + or ranges.endswith("decimal degree") + ): df.at[ix, "value"] = float(value) return df diff --git a/nmdc_runtime/api/endpoints/runs.py b/nmdc_runtime/api/endpoints/runs.py index 8b224cb5..c49b7800 100644 --- a/nmdc_runtime/api/endpoints/runs.py +++ b/nmdc_runtime/api/endpoints/runs.py @@ -42,21 +42,21 @@ def request_run( ) -def _get_run_summary(run_id, mdb): +def _get_run_summary(run_id, mdb) -> RunSummary: events_in_order = list(mdb.run_events.find({"run.id": run_id}, sort=[("time", 1)])) raise404_if_none(events_in_order or None) # TODO put relevant outputs in outputs! (for get_study_metadata job) - return { - "id": run_id, - "status": events_in_order[-1]["type"], - "started_at_time": events_in_order[0]["time"], - "was_started_by": events_in_order[0]["producer"], - "inputs": list(concat(e["inputs"] for e in events_in_order)), - "outputs": list(concat(e["outputs"] for e in events_in_order)), - "job": events_in_order[-1]["job"], - "producer": events_in_order[-1]["producer"], - "schemaURL": events_in_order[-1]["schemaURL"], - } + return RunSummary( + id=run_id, + status=events_in_order[-1]["type"], + started_at_time=events_in_order[0]["time"], + was_started_by=events_in_order[0]["producer"], + inputs=list(concat(e["inputs"] for e in events_in_order)), + outputs=list(concat(e["outputs"] for e in events_in_order)), + job=events_in_order[-1]["job"], + producer=events_in_order[-1]["producer"], + schemaURL=events_in_order[-1]["schemaURL"], + ) @router.get( diff --git a/nmdc_runtime/api/main.py b/nmdc_runtime/api/main.py index a98af373..d4a6b7f1 100644 --- a/nmdc_runtime/api/main.py +++ b/nmdc_runtime/api/main.py @@ -1,4 +1,5 @@ import os +from contextlib import asynccontextmanager from importlib import import_module import pkg_resources @@ -223,59 +224,8 @@ }, ] -app = FastAPI( - title="NMDC Runtime API", - version="0.1.0", - description=( - "This is a draft of the NMDC Runtime API." - " The resource layout currently covers aspects of workflow execution and automation," - " and is intended to facilitate discussion as more of the API is developed." - "\n\n" - "Dependency versions:\n\n" - f'nmdc-schema={pkg_resources.get_distribution("nmdc_schema").version}' - ), - openapi_tags=tags_metadata, -) -app.include_router(api_router) - - -app.add_middleware( - CORSMiddleware, - allow_origin_regex=r"(http://localhost:\d+)|(https://.+?\.microbiomedata\.org)", - allow_credentials=True, - allow_methods=["*"], - allow_headers=["*"], -) - - -@app.on_event("startup") -async def ensure_default_api_perms(): - db = get_mongo_db() - if db["_runtime.api.allow"].count_documents({}): - return - allowed = { - "/metadata/changesheets:submit": [ - "mam", - "dwinston", - "pajau", - "montana", - "spatil", - ], - "/queries:run(query_cmd:DeleteCommand)": ["scanon", "dwinston"], - } - for doc in [ - {"username": username, "action": action} - for action, usernames in allowed.items() - for username in usernames - ]: - db["_runtime.api.allow"].replace_one(doc, doc, upsert=True) - db["_runtime.api.allow"].create_index("username") - db["_runtime.api.allow"].create_index("action") - - -@app.on_event("startup") -async def ensure_initial_resources_on_boot(): +def ensure_initial_resources_on_boot(): """ensure these resources are loaded when (re-)booting the system.""" mdb = get_mongo_db() @@ -333,8 +283,7 @@ async def ensure_initial_resources_on_boot(): minter_bootstrap() -@app.on_event("startup") -async def ensure_attribute_indexes(): +def ensure_attribute_indexes(): mdb = get_mongo_db() for collection_name, index_specs in entity_attributes_to_index.items(): for spec in index_specs: @@ -346,5 +295,64 @@ async def ensure_attribute_indexes(): mdb[collection_name].create_index([(spec, 1)], name=spec, background=True) +def ensure_default_api_perms(): + db = get_mongo_db() + if db["_runtime.api.allow"].count_documents({}): + return + + allowed = { + "/metadata/changesheets:submit": [ + "mam", + "dwinston", + "pajau", + "montana", + "spatil", + ], + "/queries:run(query_cmd:DeleteCommand)": ["scanon", "dwinston"], + } + for doc in [ + {"username": username, "action": action} + for action, usernames in allowed.items() + for username in usernames + ]: + db["_runtime.api.allow"].replace_one(doc, doc, upsert=True) + db["_runtime.api.allow"].create_index("username") + db["_runtime.api.allow"].create_index("action") + + +@asynccontextmanager +async def lifespan(app: FastAPI): + ensure_initial_resources_on_boot() + ensure_attribute_indexes() + ensure_default_api_perms() + yield + + +app = FastAPI( + title="NMDC Runtime API", + version="0.1.0", + description=( + "This is a draft of the NMDC Runtime API." + " The resource layout currently covers aspects of workflow execution and automation," + " and is intended to facilitate discussion as more of the API is developed." + "\n\n" + "Dependency versions:\n\n" + f'nmdc-schema={pkg_resources.get_distribution("nmdc_schema").version}' + ), + openapi_tags=tags_metadata, + lifespan=lifespan, +) +app.include_router(api_router) + + +app.add_middleware( + CORSMiddleware, + allow_origin_regex=r"(http://localhost:\d+)|(https://.+?\.microbiomedata\.org)", + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], +) + + if __name__ == "__main__": uvicorn.run(app, host="0.0.0.0", port=8000) diff --git a/nmdc_runtime/api/models/run.py b/nmdc_runtime/api/models/run.py index 97106896..4f7cd760 100644 --- a/nmdc_runtime/api/models/run.py +++ b/nmdc_runtime/api/models/run.py @@ -1,3 +1,4 @@ +from enum import Enum import os from functools import lru_cache from typing import List, Optional @@ -43,9 +44,16 @@ class Run(BaseModel): facets: Optional[dict] +class RunEventType(str, Enum): + REQUESTED = "REQUESTED" + STARTED = "STARTED" + FAIL = "FAIL" + COMPLETE = "COMPLETE" + + class RunSummary(OpenLineageBase): id: str - status: str + status: RunEventType started_at_time: str was_started_by: str inputs: List[str] @@ -56,7 +64,7 @@ class RunSummary(OpenLineageBase): class RunEvent(OpenLineageBase): run: Run job: JobSummary - type: str + type: RunEventType time: str inputs: Optional[List[str]] = [] outputs: Optional[List[str]] = [] @@ -81,7 +89,7 @@ def _add_run_requested_event(run_spec: RunUserSpec, mdb: MongoDatabase, user: Us pick(["id", "description"], job), {"producer": PRODUCER_URL, "schemaURL": SCHEMA_URL}, ), - type="REQUESTED", + type=RunEventType.REQUESTED, time=now(as_str=True), inputs=run_spec.inputs, ) @@ -103,7 +111,7 @@ def _add_run_started_event(run_id: str, mdb: MongoDatabase): schemaURL=SCHEMA_URL, run=requested.run, job=requested.job, - type="STARTED", + type=RunEventType.STARTED, time=now(as_str=True), ).dict() ) @@ -124,7 +132,7 @@ def _add_run_fail_event(run_id: str, mdb: MongoDatabase): schemaURL=SCHEMA_URL, run=requested.run, job=requested.job, - type="FAIL", + type=RunEventType.FAIL, time=now(as_str=True), ).dict() ) @@ -145,7 +153,7 @@ def _add_run_complete_event(run_id: str, mdb: MongoDatabase, outputs: List[str]) schemaURL=SCHEMA_URL, run=started.run, job=started.job, - type="COMPLETE", + type=RunEventType.COMPLETE, time=now(as_str=True), outputs=outputs, ).dict() diff --git a/nmdc_runtime/site/graphs.py b/nmdc_runtime/site/graphs.py index 4fc81f46..da7e23b4 100644 --- a/nmdc_runtime/site/graphs.py +++ b/nmdc_runtime/site/graphs.py @@ -10,6 +10,7 @@ gold_analysis_projects_by_study, gold_projects_by_study, gold_study, + poll_for_run_completion, run_etl, local_file_to_api_object, get_operation, @@ -20,6 +21,7 @@ filter_ops_done_object_puts, hello, mongo_stats, + submit_metadata_to_db, update_schema, filter_ops_undone_expired, construct_jobs, @@ -30,6 +32,9 @@ perform_mongo_updates, add_output_run_event, gold_biosamples_by_study, + fetch_nmdc_portal_submission_by_id, + translate_portal_submission_to_nmdc_schema_database, + validate_metadata, ) @@ -120,3 +125,24 @@ def gold_study_to_database(): outputs = export_json_to_drs(database_dict, filename) add_output_run_event(outputs) + + +@graph +def translate_metadata_submission_to_nmdc_schema_database(): + metadata_submission = fetch_nmdc_portal_submission_by_id() + database = translate_portal_submission_to_nmdc_schema_database(metadata_submission) + + validate_metadata(database) + + database_dict = nmdc_schema_object_to_dict(database) + filename = nmdc_schema_database_export_filename(metadata_submission) + outputs = export_json_to_drs(database_dict, filename) + add_output_run_event(outputs) + + +@graph +def ingest_metadata_submission(): + metadata_submission = fetch_nmdc_portal_submission_by_id() + database = translate_portal_submission_to_nmdc_schema_database(metadata_submission) + run_id = submit_metadata_to_db(database) + poll_for_run_completion(run_id) diff --git a/nmdc_runtime/site/ops.py b/nmdc_runtime/site/ops.py index 224ba3c2..dac1c711 100644 --- a/nmdc_runtime/site/ops.py +++ b/nmdc_runtime/site/ops.py @@ -23,6 +23,7 @@ Out, Output, RetryPolicy, + RetryRequested, String, op, ) @@ -46,12 +47,24 @@ Operation, UpdateOperationRequest, ) -from nmdc_runtime.api.models.run import _add_run_complete_event +from nmdc_runtime.api.models.run import ( + RunEventType, + RunSummary, + _add_run_complete_event, +) from nmdc_runtime.api.models.util import ResultT from nmdc_runtime.site.drsobjects.ingest import mongo_add_docs_result_as_dict from nmdc_runtime.site.drsobjects.registration import specialize_activity_set_docs -from nmdc_runtime.site.resources import GoldApiClient, RuntimeApiSiteClient +from nmdc_runtime.site.resources import ( + NmdcPortalApiClient, + GoldApiClient, + RuntimeApiSiteClient, + RuntimeApiUserClient, +) from nmdc_runtime.site.translation.gold_translator import GoldStudyTranslator +from nmdc_runtime.site.translation.submission_portal_translator import ( + SubmissionPortalTranslator, +) from nmdc_runtime.site.util import collection_indexed_on_id, run_and_log from nmdc_runtime.util import drs_object_in_for, pluralize, put_object from nmdc_runtime.util import get_nmdc_jsonschema_dict @@ -274,6 +287,38 @@ def create_objects_from_ops(context, op_docs: list): return op_docs +@op(required_resource_keys={"runtime_api_user_client"}) +def validate_metadata(context: OpExecutionContext, database: nmdc.Database): + client: RuntimeApiUserClient = context.resources.runtime_api_user_client + response = client.validate_metadata(database) + body = response.json() + if body["result"] != "All Okay!": + raise Failure( + description="Metadata did not validate", + metadata={"detail": body["detail"]}, + ) + return body + + +@op(required_resource_keys={"runtime_api_user_client"}) +def submit_metadata_to_db(context: OpExecutionContext, database: nmdc.Database) -> str: + client: RuntimeApiUserClient = context.resources.runtime_api_user_client + response = client.submit_metadata(database) + body = response.json() + return body["detail"]["run_id"] + + +@op(required_resource_keys={"runtime_api_user_client"}) +def poll_for_run_completion(context: OpExecutionContext, run_id: str) -> RunSummary: + client: RuntimeApiUserClient = context.resources.runtime_api_user_client + response = client.get_run_info(run_id) + body = RunSummary.parse_obj(response.json()) + context.log.info(body.status) + if body.status != RunEventType.COMPLETE: + raise RetryRequested(max_retries=12, seconds_to_wait=10) + return body + + @op def filter_ops_done_object_puts() -> str: return json_util.dumps( @@ -581,7 +626,6 @@ def nmdc_schema_database_from_gold_study( def id_minter(*args, **kwargs): response = client.mint_id(*args, **kwargs) - response.raise_for_status() return response.json() translator = GoldStudyTranslator( @@ -591,9 +635,40 @@ def id_minter(*args, **kwargs): return database +@op( + required_resource_keys={"nmdc_portal_api_client"}, + config_schema={"submission_id": str}, +) +def fetch_nmdc_portal_submission_by_id(context: OpExecutionContext) -> Dict[str, Any]: + submission_id = context.op_config["submission_id"] + client: NmdcPortalApiClient = context.resources.nmdc_portal_api_client + return client.fetch_metadata_submission(submission_id) + + +@op(required_resource_keys={"runtime_api_site_client"}) +def translate_portal_submission_to_nmdc_schema_database( + context: OpExecutionContext, + metadata_submission: Dict[str, Any], +) -> nmdc.Database: + client: RuntimeApiSiteClient = context.resources.runtime_api_site_client + + def id_minter(*args, **kwargs): + response = client.mint_id(*args, **kwargs) + return response.json() + + translator = SubmissionPortalTranslator(metadata_submission, id_minter=id_minter) + database = translator.get_database() + return database + + @op -def nmdc_schema_database_export_filename(gold_study: Dict[str, Any]) -> str: - return f"database_from_{gold_study.get('studyGoldId')}.json" +def nmdc_schema_database_export_filename(study: Dict[str, Any]) -> str: + source_id = None + if "id" in study: + source_id = study["id"] + elif "studyGoldId" in study: + source_id = study["studyGoldId"] + return f"database_from_{source_id}.json" @op @@ -625,7 +700,10 @@ def export_json_to_drs( AssetMaterialization( asset_key=filename, description=description, - metadata={"drs_object_id": drs_object["id"]}, + metadata={ + "drs_object_id": MetadataValue.text(drs_object["id"]), + "json": MetadataValue.json(data), + }, ) ) return ["/objects/" + drs_object["id"]] diff --git a/nmdc_runtime/site/repository.py b/nmdc_runtime/site/repository.py index 08975aae..c3ce5e74 100644 --- a/nmdc_runtime/site/repository.py +++ b/nmdc_runtime/site/repository.py @@ -22,6 +22,8 @@ from nmdc_runtime.api.models.trigger import Trigger from nmdc_runtime.site.export.study_metadata import export_study_biosamples_metadata from nmdc_runtime.site.graphs import ( + translate_metadata_submission_to_nmdc_schema_database, + ingest_metadata_submission, gold_study_to_database, gold_translation, gold_translation_curation, @@ -35,6 +37,8 @@ from nmdc_runtime.site.resources import ( get_mongo, runtime_api_site_client_resource, + runtime_api_user_client_resource, + nmdc_portal_api_client_resource, gold_api_client_resource, terminus_resource, mongo_resource, @@ -50,6 +54,8 @@ resource_defs = { "runtime_api_site_client": runtime_api_site_client_resource, + "runtime_api_user_client": runtime_api_user_client_resource, + "nmdc_portal_api_client": nmdc_portal_api_client_resource, "gold_api_client": gold_api_client_resource, "terminus": terminus_resource, "mongo": mongo_resource, @@ -66,6 +72,13 @@ "client_secret": {"env": "API_SITE_CLIENT_SECRET"}, }, }, + "runtime_api_user_client": { + "config": { + "base_url": {"env": "API_HOST"}, + "username": {"env": "API_ADMIN_USER"}, + "password": {"env": "API_ADMIN_PASS"}, + }, + }, "mongo": { "config": { "host": {"env": "MONGO_HOST"}, @@ -449,41 +462,78 @@ def test_translation(): @repository def biosample_submission_ingest(): + normal_resources = run_config_frozen__normal_env["resources"] return [ gold_study_to_database.to_job( resource_defs=resource_defs, config={ - "resources": { - "gold_api_client": { - "config": { - "base_url": {"env": "GOLD_API_BASE_URL"}, - "username": {"env": "GOLD_API_USERNAME"}, - "password": {"env": "GOLD_API_PASSWORD"}, + "resources": merge( + unfreeze(normal_resources), + { + "gold_api_client": { + "config": { + "base_url": {"env": "GOLD_API_BASE_URL"}, + "username": {"env": "GOLD_API_USERNAME"}, + "password": {"env": "GOLD_API_PASSWORD"}, + }, }, }, - "mongo": { - "config": { - "host": {"env": "MONGO_HOST"}, - "username": {"env": "MONGO_USERNAME"}, - "password": {"env": "MONGO_PASSWORD"}, - "dbname": {"env": "MONGO_DBNAME"}, - }, + ), + "ops": { + "get_gold_study_pipeline_inputs": {"config": {"study_id": ""}}, + "export_json_to_drs": {"config": {"username": ""}}, + }, + }, + ), + translate_metadata_submission_to_nmdc_schema_database.to_job( + description="This job fetches a submission portal entry and translates it into an equivalent nmdc:Database object. The object is serialized to JSON and stored in DRS. This can be considered a dry-run for the `ingest_metadata_submission` job.", + resource_defs=resource_defs, + config={ + "resources": merge( + unfreeze(normal_resources), + { + "nmdc_portal_api_client": { + "config": { + "base_url": {"env": "NMDC_PORTAL_API_BASE_URL"}, + "session_cookie": { + "env": "NMDC_PORTAL_API_SESSION_COOKIE" + }, + } + } }, - "runtime_api_site_client": { - "config": { - "base_url": {"env": "API_HOST"}, - "site_id": {"env": "API_SITE_ID"}, - "client_id": {"env": "API_SITE_CLIENT_ID"}, - "client_secret": {"env": "API_SITE_CLIENT_SECRET"}, - }, + ), + "ops": { + "export_json_to_drs": {"config": {"username": "..."}}, + "fetch_nmdc_portal_submission_by_id": { + "config": {"submission_id": "..."} }, }, + }, + ), + ingest_metadata_submission.to_job( + description="This job fetches a submission portal entry and translates it into an equivalent nmdc:Database object. This object is validated and ingested into Mongo via a `POST /metadata/json:submit` request.", + resource_defs=resource_defs, + config={ + "resources": merge( + unfreeze(normal_resources), + { + "nmdc_portal_api_client": { + "config": { + "base_url": {"env": "NMDC_PORTAL_API_BASE_URL"}, + "session_cookie": { + "env": "NMDC_PORTAL_API_SESSION_COOKIE" + }, + } + } + }, + ), "ops": { - "get_gold_study_pipeline_inputs": {"config": {"study_id": ""}}, - "export_json_to_drs": {"config": {"username": ""}}, + "fetch_nmdc_portal_submission_by_id": { + "config": {"submission_id": "..."} + }, }, }, - ) + ), ] diff --git a/nmdc_runtime/site/resources.py b/nmdc_runtime/site/resources.py index 46787020..439fbc4d 100644 --- a/nmdc_runtime/site/resources.py +++ b/nmdc_runtime/site/resources.py @@ -15,6 +15,7 @@ ) from fastjsonschema import JsonSchemaValueException from frozendict import frozendict +from linkml_runtime.dumpers import json_dumper from pydantic import BaseModel from pymongo import MongoClient, ReplaceOne, InsertOne from terminusdb_client import WOQLClient @@ -26,18 +27,33 @@ from nmdc_runtime.api.models.operation import ListOperationsResponse from nmdc_runtime.api.models.util import ListRequest from nmdc_runtime.util import unfreeze, nmdc_jsonschema_validator_noidpatterns +from nmdc_schema import nmdc -class RuntimeApiSiteClient: - def __init__(self, base_url: str, site_id: str, client_id: str, client_secret: str): +class RuntimeApiClient: + def __init__(self, base_url: str): self.base_url = base_url - self.site_id = site_id - self.client_id = client_id - self.client_secret = client_secret self.headers = {} self.token_response = None self.refresh_token_after = None - self.get_token() + + def ensure_token(self): + if self.refresh_token_after is None or has_passed(self.refresh_token_after): + self.get_token() + + def get_token_request_body(self): + raise NotImplementedError() + + def get_token(self): + rv = requests.post(self.base_url + "/token", data=self.get_token_request_body()) + self.token_response = rv.json() + if "access_token" not in self.token_response: + raise Exception(f"Getting token failed: {self.token_response}") + + self.headers["Authorization"] = f'Bearer {self.token_response["access_token"]}' + self.refresh_token_after = expiry_dt_from_now( + **self.token_response["expires"] + ) - timedelta(seconds=5) def request(self, method, url_path, params_or_json_data=None): self.ensure_token() @@ -52,27 +68,47 @@ def request(self, method, url_path, params_or_json_data=None): rv.raise_for_status() return rv - def get_token(self): - rv = requests.post( - self.base_url + "/token", - data={ - "grant_type": "client_credentials", - "client_id": self.client_id, - "client_secret": self.client_secret, - }, - ) - self.token_response = rv.json() - if "access_token" not in self.token_response: - raise Exception(f"Getting token failed: {self.token_response}") - self.headers["Authorization"] = f'Bearer {self.token_response["access_token"]}' - self.refresh_token_after = expiry_dt_from_now( - **self.token_response["expires"] - ) - timedelta(seconds=5) +class RuntimeApiUserClient(RuntimeApiClient): + def __init__(self, username: str, password: str, *args, **kwargs): + super().__init__(*args, **kwargs) + self.username = username + self.password = password - def ensure_token(self): - if has_passed(self.refresh_token_after): - self.get_token() + def get_token_request_body(self): + return { + "grant_type": "password", + "username": self.username, + "password": self.password, + } + + def submit_metadata(self, database: nmdc.Database): + body = json_dumper.to_dict(database) + return self.request("POST", "/metadata/json:submit", body) + + def validate_metadata(self, database: nmdc.Database): + body = json_dumper.to_dict(database) + return self.request("POST", "/metadata/json:validate", body) + + def get_run_info(self, run_id: str): + return self.request("GET", f"/runs/{run_id}") + + +class RuntimeApiSiteClient(RuntimeApiClient): + def __init__( + self, site_id: str, client_id: str, client_secret: str, *args, **kwargs + ): + super().__init__(*args, **kwargs) + self.site_id = site_id + self.client_id = client_id + self.client_secret = client_secret + + def get_token_request_body(self): + return { + "grant_type": "client_credentials", + "client_id": self.client_id, + "client_secret": self.client_secret, + } def put_object_in_site(self, object_in): return self.request("POST", f"/sites/{self.site_id}:putObject", object_in) @@ -177,6 +213,21 @@ def runtime_api_site_client_resource(context): ) +@resource( + config_schema={ + "base_url": StringSource, + "username": StringSource, + "password": StringSource, + } +) +def runtime_api_user_client_resource(context): + return RuntimeApiUserClient( + base_url=context.resource_config["base_url"], + username=context.resource_config["username"], + password=context.resource_config["password"], + ) + + @lru_cache def get_runtime_api_site_client(run_config: frozendict): resource_context = build_init_resource_context( @@ -256,6 +307,35 @@ def gold_api_client_resource(context: InitResourceContext): ) +@dataclass +class NmdcPortalApiClient: + base_url: str + # Using a cookie for authentication is not ideal and should be replaced + # when this API has an another authentication method + session_cookie: str + + def fetch_metadata_submission(self, id: str) -> Dict[str, Any]: + response = requests.get( + f"{self.base_url}/api/metadata_submission/{id}", + cookies={"session": self.session_cookie}, + ) + response.raise_for_status() + return response.json() + + +@resource( + config_schema={ + "base_url": StringSource, + "session_cookie": StringSource, + } +) +def nmdc_portal_api_client_resource(context: InitResourceContext): + return NmdcPortalApiClient( + base_url=context.resource_config["base_url"], + session_cookie=context.resource_config["session_cookie"], + ) + + class MongoDB: def __init__( self, diff --git a/nmdc_runtime/site/translation/gold_translator.py b/nmdc_runtime/site/translation/gold_translator.py index 235e66bd..8806ed03 100644 --- a/nmdc_runtime/site/translation/gold_translator.py +++ b/nmdc_runtime/site/translation/gold_translator.py @@ -1,22 +1,9 @@ import collections import re -from typing import Any, Callable, Dict, List, Optional, Union +from typing import List, Union from nmdc_schema import nmdc -JSON_OBJECT = Dict[str, Any] - - -class Translator: - def __init__( - self, id_minter: Optional[Callable[[str, Optional[int]], List[str]]] = None - ) -> None: - self._id_minter = id_minter - - def _index_by_id(self, collection, id): - return {item[id]: item for item in collection} - - def _get_curie(self, prefix: str, local: str) -> str: - return f"{prefix}:{local}" +from nmdc_runtime.site.translation.translator import JSON_OBJECT, Translator class GoldStudyTranslator(Translator): diff --git a/nmdc_runtime/site/translation/submission_portal_translator.py b/nmdc_runtime/site/translation/submission_portal_translator.py new file mode 100644 index 00000000..90fb225b --- /dev/null +++ b/nmdc_runtime/site/translation/submission_portal_translator.py @@ -0,0 +1,442 @@ +import logging +import re +from typing import Any, List, Optional, Union +from nmdc_runtime.site.translation.translator import JSON_OBJECT, Translator +from nmdc_schema import nmdc +from toolz import get_in, groupby, concat +from importlib import resources +from linkml_runtime import SchemaView +from linkml_runtime.linkml_model import SlotDefinition +from functools import lru_cache + + +@lru_cache +def _get_schema_view(): + """Return a SchemaView instance representing the NMDC schema""" + return SchemaView( + str(resources.path("nmdc_schema", "nmdc_materialized_patterns.yaml")) + ) + + +class SubmissionPortalTranslator(Translator): + """A Translator subclass for handling submission portal entries + + This translator is constructed with a metadata_submission object from the + submission portal. Since the submission schema is built by importing slots + from the nmdc:Biosample class this translator largely works by introspecting + the nmdc:Biosample class (via a SchemaView instance) + """ + + def __init__(self, metadata_submission: JSON_OBJECT = {}, *args, **kwargs) -> None: + super().__init__(*args, **kwargs) + + self.metadata_submission = metadata_submission + self.schema_view: SchemaView = _get_schema_view() + + def _get_pi( + self, metadata_submission: JSON_OBJECT + ) -> Union[nmdc.PersonValue, None]: + """Construct an nmdc:PersonValue object using values from the study form data + + :param metadata_submission: submission portal entry + :return: nmdc:PersonValue + """ + study_form = metadata_submission.get("studyForm") + if not study_form: + return None + + return nmdc.PersonValue( + name=study_form.get("piName"), + email=study_form.get("piEmail"), + orcid=study_form.get("piOrcid"), + ) + + def _get_doi( + self, metadata_submission: JSON_OBJECT + ) -> Union[nmdc.AttributeValue, None]: + """Construct an nmdc:AttributeValue object using information from the context form data + + :param metadata_submission: submission portal entry + :return: nmdc:AttributeValue + """ + doi = get_in(["contextForm", "datasetDoi"], metadata_submission) + if not doi: + return None + + return nmdc.AttributeValue(has_raw_value=doi) + + def _get_has_credit_associations( + self, metadata_submission: JSON_OBJECT + ) -> Union[List[nmdc.CreditAssociation], None]: + """Construct a list of nmdc:CreditAssociation from the study form data + + :param metadata_submission: submission portal entry + :return: nmdc.CreditAssociation list + """ + contributors = get_in(["studyForm", "contributors"], metadata_submission) + if not contributors: + return None + + return [ + nmdc.CreditAssociation( + applies_to_person=nmdc.PersonValue( + name=contributor.get("name"), + orcid=contributor.get("orcid"), + ), + applied_roles=contributor.get("roles"), + ) + for contributor in contributors + ] + + def _get_gold_study_identifiers( + self, metadata_submission: JSON_OBJECT + ) -> Union[List[str], None]: + """Construct a GOLD CURIE from the multiomics from data + + :param metadata_submission: submission portal entry + :return: GOLD CURIE + """ + gold_study_id = get_in(["multiOmicsForm", "GOLDStudyId"], metadata_submission) + if not gold_study_id: + return None + + return [self._get_curie("GOLD", gold_study_id)] + + def _get_quantity_value( + self, raw_value: Optional[str], unit: Optional[str] = None + ) -> Union[nmdc.QuantityValue, None]: + """Construct a nmdc:QuantityValue from a raw value string + + The regex pattern minimally matches on a single numeric value (possibly + floating point). The pattern can also identify a range represented by + two numeric values separated by a hyphen. It can also identify non-numeric + characters at the end of the string which are interpreted as a unit. A unit + may also be explicitly provided as an argument to this function. If parsing + identifies a unit and a unit argument is provided, the unit argument is used. + If the pattern is not matched at all None is returned. + + TODO: currently the parsed unit string is used as-is. In the future we may want + to be stricter about what we accept or coerce into a controlled value set + + :param raw_value: string to parse + :param unit: optional unit, defaults to None + :return: nmdc:QuantityValue + """ + if raw_value is None: + return None + + match = re.fullmatch( + "([+-]?(?=\.\d|\d)(?:\d+)?(?:\.?\d*)(?:[eE][+-]?\d+)?)(?: *- *([+-]?(?=\.\d|\d)(?:\d+)?(?:\.?\d*)(?:[eE][+-]?\d+)?))?(?: *(\S+))?", + raw_value, + ) + if not match: + return None + + qv = nmdc.QuantityValue(has_raw_value=raw_value) + if match.group(2): + # having group 2 means the value is a range like "0 - 1". Either + # group 1 or group 2 might be the minimum especially when handling + # negative ranges like "0 - -1" + num_1 = float(match.group(1)) + num_2 = float(match.group(2)) + qv.has_minimum_numeric_value = min(num_1, num_2) + qv.has_maximum_numeric_value = max(num_1, num_2) + else: + # otherwise we just have a single numeric value + qv.has_numeric_value = float(match.group(1)) + + if unit: + # a unit was manually specified + if match.group(3) and unit != match.group(3): + # a unit was also found in the raw string; issue a warning + # if they don't agree, but keep the manually specified one + logging.warning(f'Unit mismatch: "{unit}" and "{match.group(3)}"') + qv.has_unit = unit + elif match.group(3): + # a unit was found in the raw string + qv.has_unit = match.group(3) + + return qv + + def _get_ontology_class( + self, raw_value: Optional[str] + ) -> Union[nmdc.OntologyClass, None]: + """Construct a nmdc:OntologyClass from a raw value string + + The regexp pattern matches values of the format "name [identifier]". If this pattern is + not matched None is returned. + + :param raw_value: string to parse + :return: nmdc.OntologyClass + """ + match = re.fullmatch("_*([^\[]+)(?:\[([^\]]+)\])", raw_value) + if not match or not match.group(2): + logging.warning( + f'Could not infer OntologyClass id from value "{raw_value}"' + ) + return None + + return nmdc.OntologyClass( + name=match.group(1).strip(), + id=match.group(2).strip(), + ) + + def _get_controlled_identified_term_value( + self, raw_value: Optional[str] + ) -> Union[nmdc.ControlledIdentifiedTermValue, None]: + """Construct a nmdc.ControlledIdentifiedTermValue from a raw value string + + The regexp pattern matches values of the format "name [identifier]". If this pattern is + not matched None is returned. + + :param raw_value: string to parse + :return: nmdc.ControlledIdentifiedTermValue + """ + if not raw_value: + return None + + ontology_class = self._get_ontology_class(raw_value) + if ontology_class is None: + return None + + return nmdc.ControlledIdentifiedTermValue( + has_raw_value=raw_value, term=ontology_class + ) + + def _get_controlled_term_value( + self, raw_value: Optional[str] + ) -> Union[nmdc.ControlledTermValue, None]: + """Construct a nmdc.ControlledTermValue from a raw value string + + The regexp pattern matches values of the format "name [identifier]". The identifier portion + is optional. If it is not found then the returned object's `term` field will be none. + + :param raw_value: string to parse + :return: nmdc.ControlledTermValue + """ + if not raw_value: + return None + + value = nmdc.ControlledTermValue(has_raw_value=raw_value) + ontology_class = self._get_ontology_class(raw_value) + if ontology_class is not None: + value.term = ontology_class + + return value + + def _get_geolocation_value( + self, raw_value: Optional[str] + ) -> Union[nmdc.GeolocationValue, None]: + """Construct a nmdc.GeolocationValue from a raw string value + + The regexp pattern matches a latitude and a longitude value separated by a space or comma. The + latitude and longitude values should be in decimal degrees. If the pattern is not matched, None + is returned. + + :param raw_value: string to parse + :return: nmdc.GeolocationValue + """ + if raw_value is None: + return None + + match = re.fullmatch( + "([-+]?(?:[1-8]?\d(?:\.\d+)?|90(?:\.0+)?))[\s,]+([-+]?(?:180(?:\.0+)?|(?:(?:1[0-7]\d)|(?:[1-9]?\d))(?:\.\d+)?))", + raw_value, + ) + if match is None: + return None + + return nmdc.GeolocationValue( + has_raw_value=raw_value, latitude=match.group(1), longitude=match.group(2) + ) + + def _get_float(self, raw_value: Optional[str]) -> Union[float, None]: + """Construct a float from a raw string value + + If a float cannot be parsed from the string, None is returned. + + :param raw_value: string to parse + :return: float + """ + try: + return float(raw_value) + except (ValueError, TypeError): + return None + + def _get_from(self, metadata_submission: JSON_OBJECT, field: Union[str, List[str]]): + """Extract and sanitize a value from a nested dict + + For field = [i0, i1, ..., iN] extract metadata_submission[i0][i1]...[iN]. This + value is then sanitized by trimming strings, replacing empty strings with None, + filtering Nones and empty strings from arrays. + + :param metadata_submission: submission portal entry + :param field: list of nested fields to extract + :return: sanitized value + """ + if not isinstance(field, list): + field = [field] + value = get_in(field, metadata_submission) + + def sanitize(val): + sanitized = val + if isinstance(sanitized, str): + sanitized = sanitized.strip() + if sanitized == "": + sanitized = None + return sanitized + + if isinstance(value, list): + value = [sanitize(v) for v in value] + value = [v for v in value if v is not None] + if not value: + value = None + else: + value = sanitize(value) + + return value + + def _translate_study( + self, metadata_submission: JSON_OBJECT, nmdc_study_id: str + ) -> nmdc.Study: + """Translate a metadata submission into an `nmdc:Study` object. + + This method translates a metadata submission object into an equivalent + `nmdc:Study` object. The minted NMDC study ID must be passed to this method. + + :param gold_study: metadata submission object + :param nmdc_study_id: Minted nmdc:Study identifier for the translated object + :return: nmdc:Study object + """ + return nmdc.Study( + alternative_identifiers=self._get_from( + metadata_submission, ["multiOmicsForm", "JGIStudyId"] + ), + alternative_names=self._get_from( + metadata_submission, ["multiOmicsForm", "alternativeNames"] + ), + description=self._get_from( + metadata_submission, ["studyForm", "description"] + ), + doi=self._get_doi(metadata_submission), + emsl_proposal_identifier=self._get_from( + metadata_submission, ["multiOmicsForm", "studyNumber"] + ), + gold_study_identifiers=self._get_gold_study_identifiers( + metadata_submission + ), + has_credit_associations=self._get_has_credit_associations( + metadata_submission + ), + id=nmdc_study_id, + insdc_bioproject_identifiers=self._get_from( + metadata_submission, ["multiOmicsForm", "NCBIBioProjectId"] + ), + name=self._get_from(metadata_submission, ["studyForm", "studyName"]), + notes=self._get_from(metadata_submission, ["studyForm", "notes"]), + principal_investigator=self._get_pi(metadata_submission), + title=self._get_from(metadata_submission, ["studyForm", "studyName"]), + websites=self._get_from( + metadata_submission, ["studyForm", "linkOutWebpage"] + ), + ) + + def _transform_value_for_slot(self, value: Any, slot: SlotDefinition): + transformed_value = None + if slot.range == "TextValue": + transformed_value = nmdc.TextValue(has_raw_value=value) + elif slot.range == "QuantityValue": + transformed_value = self._get_quantity_value(value) + elif slot.range == "ControlledIdentifiedTermValue": + transformed_value = self._get_controlled_identified_term_value(value) + elif slot.range == "ControlledTermValue": + transformed_value = self._get_controlled_term_value(value) + elif slot.range == "TimestampValue": + transformed_value = nmdc.TimestampValue(has_raw_value=value) + elif slot.range == "GeolocationValue": + transformed_value = self._get_geolocation_value(value) + elif slot.range == "float": + transformed_value = self._get_float(value) + elif slot.range == "string": + transformed_value = str(value).strip() + else: + transformed_value = value + + return transformed_value + + def _translate_biosample( + self, sample_data: List[JSON_OBJECT], nmdc_biosample_id: str, nmdc_study_id: str + ) -> nmdc.Biosample: + """Translate sample data from portal submission into an `nmdc:Biosample` object. + + sample_data is a list of objects where each object represents one row from a tab in + the submission portal. Each of the objects represent information about the same + underlying biosample. For each of the rows, each of the columns is iterated over. + For each column, the corresponding slot from the nmdc:Biosample class is identified. + The raw value from the submission portal is the transformed according to the range + of the nmdc:Biosample slot. + + :param sample_data: collection of rows representing data about a single biosample + from each applicable submission portal tab + :param nmdc_biosample_id: Minted nmdc:Biosample identifier for the translated object + :param nmdc_study_id: Minted nmdc:Study identifier for the related Study + :return: nmdc:Biosample + """ + slots = {"id": nmdc_biosample_id, "part_of": nmdc_study_id} + biosample_slot_names = self.schema_view.class_slots("Biosample") + for tab in sample_data: + for column, value in tab.items(): + if column not in biosample_slot_names: + logging.warning(f"No slot {column} on nmdc:Biosample") + continue + slot = self.schema_view.induced_slot(column, "Biosample") + + transformed_value = None + if slot.multivalued: + transformed_value = [ + self._transform_value_for_slot(item, slot) for item in value + ] + else: + transformed_value = self._transform_value_for_slot(value, slot) + + slots[column] = transformed_value + + return nmdc.Biosample(**slots) + + def get_database(self) -> nmdc.Database: + """Translate the submission portal entry to an nmdc:Database + + This method translates the submission portal entry into one nmdc:Study and a set + of nmdc:Biosample objects. THese are wrapped into an nmdc:Database. NMDC identifiers + are minted for each new object. + + :return: nmdc:Database object + """ + database = nmdc.Database() + + nmdc_study_id = self._id_minter("nmdc:Study")[0] + + metadata_submission_data = self.metadata_submission.get( + "metadata_submission", {} + ) + database.study_set = [ + self._translate_study(metadata_submission_data, nmdc_study_id) + ] + + sample_data = metadata_submission_data.get("sampleData", {}) + sample_data_by_id = groupby("source_mat_id", concat(sample_data.values())) + nmdc_biosample_ids = self._id_minter("nmdc:Biosample", len(sample_data_by_id)) + sample_data_to_nmdc_biosample_ids = dict( + zip(sample_data_by_id.keys(), nmdc_biosample_ids) + ) + + database.biosample_set = [ + self._translate_biosample( + sample_data, + sample_data_to_nmdc_biosample_ids[sample_data_id], + nmdc_study_id, + ) + for sample_data_id, sample_data in sample_data_by_id.items() + ] + + return database diff --git a/nmdc_runtime/site/translation/translator.py b/nmdc_runtime/site/translation/translator.py new file mode 100644 index 00000000..41987796 --- /dev/null +++ b/nmdc_runtime/site/translation/translator.py @@ -0,0 +1,22 @@ +from abc import ABC, abstractmethod +from typing import Any, Callable, Dict, List, Optional +from nmdc_schema import nmdc + +JSON_OBJECT = Dict[str, Any] + + +class Translator(ABC): + def __init__( + self, id_minter: Optional[Callable[[str, Optional[int]], List[str]]] = None + ) -> None: + self._id_minter = id_minter + + def _index_by_id(self, collection, id): + return {item[id]: item for item in collection} + + def _get_curie(self, prefix: str, local: str) -> str: + return f"{prefix}:{local}" + + @abstractmethod + def get_database(self) -> nmdc.Database: + pass diff --git a/setup.py b/setup.py index 96ab0cb5..20c936ad 100644 --- a/setup.py +++ b/setup.py @@ -4,12 +4,6 @@ with open("README.md") as f: long_description = f.read() -with open("requirements/main.in") as f: - install_requires = f.read().splitlines() - -with open("requirements/dev.in") as f: - dev_requires = f.read().splitlines()[1:] # Elide `-c main.txt` constraint - setup( name="nmdc_runtime", url="https://github.com/microbiomedata/nmdc-runtime", @@ -29,10 +23,6 @@ "Programming Language :: Python :: 3", "License :: OSI Approved :: Apache Software License", ], - install_requires=install_requires, - extras_require={ - "dev": dev_requires, - }, python_requires=">=3.10", entry_points={ "console_scripts": [ diff --git a/tests/files/nmdc:bsm-11-5nhz3402.json b/tests/files/nmdc:bsm-11-5nhz3402.json new file mode 100644 index 00000000..ead62f2f --- /dev/null +++ b/tests/files/nmdc:bsm-11-5nhz3402.json @@ -0,0 +1,66 @@ +{ + "elev": 1, + "specific_ecosystem": "Bulk soil", + "env_medium": { + "has_raw_value": "ENVO_00005802", + "term": { + "id": "ENVO:00005802", + "name": "bulk soil" + } + }, + "habitat": "Soil", + "ecosystem_category": "Terrestrial", + "img_identifiers": [ + "img.taxon:3300046656" + ], + "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33 soil", + "geo_loc_name": { + "has_raw_value": "USA: Oregon" + }, + "lat_lon": { + "has_raw_value": "46.1208 -123.2695", + "latitude": 46.1208, + "longitude": -123.2695 + }, + "env_local_scale": { + "has_raw_value": "ENVO_00000011", + "term": { + "id": "ENVO:00000011", + "name": "garden" + } + }, + "location": "USA", + "ecosystem_type": "Soil", + "ncbi_taxonomy_name": "soil metagenome", + "ecosystem": "Environmental", + "mod_date": "2021-05-01T00:00:00", + "env_broad_scale": { + "has_raw_value": "ENVO_00000446", + "term": { + "id": "ENVO:00000446", + "name": "terrestrial biome" + } + }, + "samp_taxon_id": { + "has_raw_value": "soil metagenome [NCBITaxon:410658]" + }, + "id": "nmdc:bsm-11-5nhz3402", + "add_date": "2021-05-01T00:00:00", + "sample_collection_site": "Bulk Soil", + "collected_from": "nmdc:frsite-11-5tz5zk13", + "depth": { + "has_raw_value": "0.1", + "has_numeric_value": 0.1, + "has_unit": "meters" + }, + "part_of": [ + "nmdc:sty-11-r2h77870" + ], + "gold_biosample_identifiers": [ + "GOLD:Gb0291582" + ], + "samp_name": "BESC-13-CL1_35_33 soil", + "ecosystem_subtype": "Botanical garden", + "type": "nmdc:Biosample", + "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA" +} diff --git a/tests/files/test_changesheet_update_one_ph.tsv b/tests/files/test_changesheet_update_one_ph.tsv new file mode 100644 index 00000000..61bcd438 --- /dev/null +++ b/tests/files/test_changesheet_update_one_ph.tsv @@ -0,0 +1,2 @@ +id action attribute value +nmdc:bsm-11-5nhz3402 update ph 5.58 \ No newline at end of file diff --git a/tests/test_api/test_metadata.py b/tests/test_api/test_metadata.py index d9b2d79d..efdca014 100644 --- a/tests/test_api/test_metadata.py +++ b/tests/test_api/test_metadata.py @@ -5,6 +5,8 @@ import fastjsonschema import pandas as pd import pytest + +from nmdc_runtime.api.db.mongo import get_mongo_db from nmdc_runtime.util import get_nmdc_jsonschema_dict from toolz import dissoc @@ -142,6 +144,23 @@ def test_update_pi_websites(): assert first_result["doc_after"]["principal_investigator"] == pi_info +def test_update_biosample_ph(): + mdb = get_mongo_db() + doc = json.loads( + (REPO_ROOT_DIR / "tests" / "files" / "nmdc:bsm-11-5nhz3402.json").read_text() + ) + mdb.biosample_set.replace_one({"id": "nmdc:bsm-11-5nhz3402"}, doc, upsert=True) + df = load_changesheet( + (REPO_ROOT_DIR / "tests" / "files" / "test_changesheet_update_one_ph.tsv"), mdb + ) + + update_cmd = mongo_update_command_for(df) + + assert isinstance( + update_cmd["nmdc:bsm-11-5nhz3402"]["updates"][0]["u"]["$set"]["ph"], float + ) + + def test_ensure_data_object_type(): docs_test = { "data_object_set": [ diff --git a/tests/test_data/conftest.py b/tests/test_data/conftest.py new file mode 100644 index 00000000..331183bd --- /dev/null +++ b/tests/test_data/conftest.py @@ -0,0 +1,19 @@ +import pytest +import uuid +import random + + +@pytest.fixture +def test_minter(): + def mint(type, how_many=1): + return [ + "fake:" + + str( + uuid.UUID( + bytes=bytes(random.getrandbits(8) for _ in range(16)), version=4 + ) + ) + for _ in range(how_many) + ] + + return mint diff --git a/tests/test_data/test_gold_translator.py b/tests/test_data/test_gold_translator.py index fa5b977f..30ebb251 100644 --- a/tests/test_data/test_gold_translator.py +++ b/tests/test_data/test_gold_translator.py @@ -1,11 +1,8 @@ -import json import random -import uuid from pathlib import Path import yaml from nmdc_schema import nmdc -from linkml_runtime.dumpers import json_dumper, yaml_dumper from nmdc_runtime.site.translation.gold_translator import GoldStudyTranslator @@ -426,18 +423,7 @@ def test_get_field_site_name(): assert field_site_name == "Mackenzie" -def test_get_dataset(): - def test_minter(type, how_many=1): - return [ - "fake:" - + str( - uuid.UUID( - bytes=bytes(random.getrandbits(8) for _ in range(16)), version=4 - ) - ) - for _ in range(how_many) - ] - +def test_get_dataset(test_minter): random.seed(0) with open(Path(__file__).parent / "test_gold_translator_data.yaml") as f: test_datasets = yaml.safe_load_all(f) diff --git a/tests/test_data/test_submission_portal_translator.py b/tests/test_data/test_submission_portal_translator.py new file mode 100644 index 00000000..97d815bb --- /dev/null +++ b/tests/test_data/test_submission_portal_translator.py @@ -0,0 +1,252 @@ +from pathlib import Path +import random + +import yaml +from nmdc_runtime.api.endpoints.metadata import _validate_json +from nmdc_runtime.site.translation.submission_portal_translator import ( + SubmissionPortalTranslator, +) +from nmdc_schema import nmdc + + +def test_get_pi(): + translator = SubmissionPortalTranslator() + pi_person_value = translator._get_pi( + { + "studyForm": { + "piName": "Maria D. McDonald", + "piEmail": "MariaDMcDonald@example.edu", + "piOrcid": "", + } + } + ) + assert pi_person_value is not None + assert pi_person_value.name == "Maria D. McDonald" + assert pi_person_value.email == "MariaDMcDonald@example.edu" + + pi_person_value = translator._get_pi({}) + assert pi_person_value is None + + +def test_get_doi(): + translator = SubmissionPortalTranslator() + doi = translator._get_doi({"contextForm": {"datasetDoi": "1234"}}) + assert doi is not None + assert doi.has_raw_value == "1234" + + doi = translator._get_doi({"contextForm": {"datasetDoi": ""}}) + assert doi is None + + doi = translator._get_doi({"contextForm": {}}) + assert doi is None + + +def test_get_has_credit_associations(): + translator = SubmissionPortalTranslator() + credit_associations = translator._get_has_credit_associations( + { + "studyForm": { + "contributors": [ + { + "name": "Brenda Patterson", + "orcid": "1234", + "roles": ["Conceptualization", "Data curation"], + }, + { + "name": "Lee F. Dukes", + "orcid": "5678", + "roles": ["Data curation"], + }, + ] + } + } + ) + assert credit_associations is not None + assert len(credit_associations) == 2 + assert credit_associations[0].applies_to_person is not None + assert credit_associations[0].applies_to_person.name == "Brenda Patterson" + assert credit_associations[0].applies_to_person.orcid == "1234" + assert credit_associations[0].applied_roles is not None + assert len(credit_associations[0].applied_roles) == 2 + assert credit_associations[0].applied_roles[0].code.text == "Conceptualization" + + +def test_get_quantity_value(): + translator = SubmissionPortalTranslator() + + qv = translator._get_quantity_value("3.5") + assert qv is not None + assert qv.has_raw_value == "3.5" + assert qv.has_numeric_value == 3.5 + assert qv.has_minimum_numeric_value is None + assert qv.has_maximum_numeric_value is None + assert qv.has_unit is None + + qv = translator._get_quantity_value("0-.1") + assert qv is not None + assert qv.has_raw_value == "0-.1" + assert qv.has_numeric_value is None + assert qv.has_minimum_numeric_value == 0 + assert qv.has_maximum_numeric_value == 0.1 + assert qv.has_unit is None + + qv = translator._get_quantity_value("1.2 ppm") + assert qv is not None + assert qv.has_raw_value == "1.2 ppm" + assert qv.has_numeric_value == 1.2 + assert qv.has_minimum_numeric_value is None + assert qv.has_maximum_numeric_value is None + assert qv.has_unit == "ppm" + + qv = translator._get_quantity_value("98.6F") + assert qv is not None + assert qv.has_raw_value == "98.6F" + assert qv.has_numeric_value == 98.6 + assert qv.has_minimum_numeric_value is None + assert qv.has_maximum_numeric_value is None + assert qv.has_unit == "F" + + qv = translator._get_quantity_value("-80", unit="C") + assert qv is not None + assert qv.has_raw_value == "-80" + assert qv.has_numeric_value == -80 + assert qv.has_minimum_numeric_value is None + assert qv.has_maximum_numeric_value is None + assert qv.has_unit == "C" + + qv = translator._get_quantity_value("-90 - -100m", unit="meter") + assert qv is not None + assert qv.has_raw_value == "-90 - -100m" + assert qv.has_numeric_value is None + assert qv.has_minimum_numeric_value == -100 + assert qv.has_maximum_numeric_value == -90 + assert qv.has_unit == "meter" + + +def test_get_gold_study_identifiers(): + translator = SubmissionPortalTranslator() + + gold_ids = translator._get_gold_study_identifiers( + {"multiOmicsForm": {"GOLDStudyId": "Gs000000"}} + ) + assert gold_ids is not None + assert len(gold_ids) == 1 + assert gold_ids[0] == "GOLD:Gs000000" + + gold_ids = translator._get_gold_study_identifiers( + {"multiOmicsForm": {"GOLDStudyId": ""}} + ) + assert gold_ids is None + + +def test_get_controlled_identified_term_value(): + translator = SubmissionPortalTranslator() + + value = translator._get_controlled_identified_term_value(None) + assert value is None + + value = translator._get_controlled_identified_term_value("") + assert value is None + + value = translator._get_controlled_identified_term_value("term") + assert value is None + + value = translator._get_controlled_identified_term_value("____term [id:00001]") + assert value is not None + assert value.has_raw_value == "____term [id:00001]" + assert value.term.id == "id:00001" + assert value.term.name == "term" + + +def test_get_controlled_term_value(): + translator = SubmissionPortalTranslator() + + value = translator._get_controlled_term_value(None) + assert value is None + + value = translator._get_controlled_term_value("") + assert value is None + + value = translator._get_controlled_term_value("term") + assert value is not None + assert value.has_raw_value == "term" + assert value.term is None + + value = translator._get_controlled_term_value("____term [id:00001]") + assert value is not None + assert value.has_raw_value == "____term [id:00001]" + assert value.term.id == "id:00001" + assert value.term.name == "term" + + +def test_get_geolocation_value(): + translator = SubmissionPortalTranslator() + + value = translator._get_geolocation_value("0 0") + assert value is not None + assert value.has_raw_value == "0 0" + assert value.latitude == 0 + assert value.longitude == 0 + + value = translator._get_geolocation_value("-3.903895 -38.560507") + assert value is not None + assert value.has_raw_value == "-3.903895 -38.560507" + assert value.latitude == -3.903895 + assert value.longitude == -38.560507 + + # latitude > 90 not allowed + value = translator._get_geolocation_value("93.903895 -38.560507") + assert value is None + + value = translator._get_geolocation_value("180") + assert value is None + + +def test_get_float(): + translator = SubmissionPortalTranslator() + + value = translator._get_float("-3.5332") + assert value == -3.5332 + + value = translator._get_float("") + assert value is None + + value = translator._get_float(None) + assert value is None + + +def test_get_from(): + translator = SubmissionPortalTranslator() + + metadata = { + "one": { + "two": {"three": " three ", "empty": ""}, + "four": ["one", " two ", "three"], + "empty": [""], + "some_empty": ["one", "", "three"], + } + } + assert translator._get_from(metadata, "one") == metadata["one"] + assert translator._get_from(metadata, ["one", "two", "three"]) == "three" + assert translator._get_from(metadata, ["one", "two", "empty"]) is None + assert translator._get_from(metadata, "two") is None + assert translator._get_from(metadata, ["one", "four"]) == ["one", "two", "three"] + assert translator._get_from(metadata, ["one", "empty"]) is None + assert translator._get_from(metadata, ["one", "some_empty"]) == ["one", "three"] + + +def test_get_dataset(test_minter): + random.seed(0) + with open( + Path(__file__).parent / "test_submission_portal_translator_data.yaml" + ) as f: + test_datasets = yaml.safe_load_all(f) + + for test_data in test_datasets: + translator = SubmissionPortalTranslator( + **test_data["input"], id_minter=test_minter + ) + + expected = nmdc.Database(**test_data["output"]) + actual = translator.get_database() + assert actual == expected diff --git a/tests/test_data/test_submission_portal_translator_data.yaml b/tests/test_data/test_submission_portal_translator_data.yaml new file mode 100644 index 00000000..b7562096 --- /dev/null +++ b/tests/test_data/test_submission_portal_translator_data.yaml @@ -0,0 +1,13203 @@ +--- +input: + metadata_submission: + metadata_submission: + packageName: plant-associated + contextForm: + datasetDoi: 10.46936/10.25585/60000818 + dataGenerated: true + facilityGenerated: true + facilities: [] + award: + otherAward: '' + addressForm: + shipper: + name: '' + email: '' + phone: '' + line1: '' + line2: '' + city: '' + state: '' + postalCode: '' + expectedShippingDate: + shippingConditions: '' + sample: '' + description: '' + experimentalGoals: '' + randomization: '' + usdaRegulated: + permitNumber: '' + biosafetyLevel: '' + irbOrHipaa: + comments: '' + templates: + - plant-associated + studyForm: + studyName: Seasonal activities of the phyllosphere microbiome of perennial crops + piName: Ashley Shade + piEmail: shade.ashley@gmail.com + piOrcid: 0000-0002-7189-3067 + linkOutWebpage: + - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9950430/ + studyDate: + description: Understanding the interactions between plants and microorganisms + can inform microbiome management to enhance crop productivity and resilience + to stress. Here, we apply a genome-centric approach to identify ecologically + important leaf microbiome members on replicated plots of field-grown switchgrass + and miscanthus, and to quantify their activities over two growing seasons for + switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 + medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes + represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, + and Bacteroidota) are active in the late season, and upregulate transcripts + for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide + cyclase. Stress-associated pathways are expressed for most MAGs, suggesting + engagement with the host environment. We also detect seasonally activated biosynthetic + pathways for terpenes and various non-ribosomal peptide pathways that are poorly + annotated. Our findings support that leaf-associated bacterial populations are + seasonally dynamic and responsive to host cues. + notes: '' + contributors: + - name: Adina Howe + orcid: 0000-0002-7705-343X + roles: + - Writing review and editing + - Visualization + - Writing original draft + - Investigation + - Formal Analysis + - Data curation + - Conceptualization + - Validation + - Supervision + - Project administration + - Methodology + - Resources + - Software + - Principal Investigator + - Funding acquisition + multiOmicsForm: + alternativeNames: [] + studyNumber: '' + GOLDStudyId: '' + JGIStudyId: '' + NCBIBioProjectId: '' + omicsProcessingTypes: + - mg + - mt + sampleData: + plant_associated_data: + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:e8ed34cc-32f4-4fc5-9b9f-c2699e43163c + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:774bb4b9-5ebe-48d5-8236-1a60baa6af7a + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c0bb595b-9992-4475-8019-775189b5250a + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d74181a3-6fb9-406e-89f8-2d4861a4646c + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:edfd5080-ccc2-495b-b17a-190ad6649291 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:483921c0-7fa9-4a31-b281-e09565a0d6f9 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:3b9aab19-0110-415b-8e29-849f0696de47 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:579ec4b9-57c4-4431-8df9-432138233b0b + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:69dd84ff-d777-4d1e-ac22-9cdac87074f5 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c0c4a2b5-0382-450a-8728-a176fa438efe + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c54a1438-713a-4b6f-9e44-ecddbd27e974 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:8e0225d6-f7a0-469b-a747-8f5f4d65dc69 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:1d20602f-3a0a-4d58-96cf-16135467ba14 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f13b1234-886c-4f8f-9663-850f5daff8e1 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:45c11d1c-4a00-4162-9cdb-1020966507c6 + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_09MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:76a6a11e-5e25-4270-8d0d-1701bd12517a + ecosystem_type: Plant-associated + collection_date: '2016-05-09' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:bac125d1-f295-4728-a7fd-e4911a985b44 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:13d073fa-b45a-4e47-a570-71a8a5726ac7 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:7a7c2686-18fc-4a3c-8c2c-e2a195cd0a28 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:7325ce99-4347-4728-b5aa-dda21a760a07 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:8a7956e3-0f51-4e60-8aa0-380285878c86 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:df9a0e6b-28c6-490b-aae9-559126dcd31a + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f1d3e678-eaa9-4e36-ae17-c8bed8133825 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d43c6831-cafe-4674-9e56-adf20da087f6 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:a2e9ab67-4112-447e-82a1-2c674769ef3e + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:1083f373-69b8-4ca1-9f5e-406d34781d9d + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:20ec38cc-8e1d-4b16-a08a-5e75881701d5 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f408f2c4-5c6f-43b1-b1d5-dc264317f826 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:78c5bfe7-2e39-4419-aae5-cc60ac5c6b80 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:4bcd56e0-dc05-46f4-b93c-2c548ffd0f48 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:090aa36b-b82e-4ff4-9c01-b3de17bd7720 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_31MAY2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:03aaf489-f1cc-43e4-b537-9cfd2d5fe7b6 + ecosystem_type: Plant-associated + collection_date: '2016-05-31' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:b16cb1c2-def5-45b3-aeee-1de1762fac8c + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:7635e9bf-db34-4211-abb3-53df9119fdfa + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:3558ef40-a322-4ea0-89c3-afb0cfba3199 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:96c80952-f26a-4014-8ebc-72648e90e2bb + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d0b85994-73f5-43f0-97c1-ef0ce27cae7f + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:0e8e63b0-b2ce-4f4a-af1f-a6242b44a205 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:346b2bf3-3899-44b7-88b7-38cd157a78ac + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:0e337fca-5bdc-41b9-9c2c-9c043af02850 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d43031d6-4949-4af4-ab93-0d4a52ddc41b + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:247e0564-3ba0-4aed-bc73-237038d0f273 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:99841196-4418-47c7-941a-475272baa537 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:71ce7bb9-1267-4cfd-9437-42cac3175456 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:7908e2ad-6c33-40ec-b00a-0b054560e5e3 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:5efa5fcd-8ad5-488c-9684-91a2c5dfeb21 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:de4244c9-04f2-4223-aca8-3b6753f230e2 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_20JUN2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d19bd65e-9530-44c6-9af4-9c08332c9966 + ecosystem_type: Plant-associated + collection_date: '2016-06-20' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:95f249ad-1b54-4c8f-900e-c2abf32e3836 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:b7f2fece-413f-43ea-83f3-80c01fc218c1 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:dae06229-433f-45fd-a2ef-d82712dcb14d + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:6a50b37a-10fc-4370-b2eb-c4ba33685a9e + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:99d5ad42-73d2-4eaa-a603-63e3e823ba8c + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:80fe230b-e255-4df6-875a-51dae2bfc222 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f1e2af4b-e345-4878-9cc9-b24e1007c85f + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:4a9a58de-6cb1-489d-95a6-86df4adffb23 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:9f55830a-9871-4a8a-b872-f6b8d5513a65 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:cecc6251-2151-49e2-9f55-fb5b9409cd4c + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:79d6bc42-19e6-4cbc-b394-26fff15492e5 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:93486fde-e381-4aac-86eb-2387dd44f138 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:7d9c0233-a597-407c-bdad-1c4f79a4cc6e + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f8b5663d-3322-475b-880a-29377f37f346 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c07f456e-d797-437c-9b79-11e16494e90d + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_12JUL2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:913a098d-20e6-4581-b657-fc07701d5d44 + ecosystem_type: Plant-associated + collection_date: '2016-07-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:726e08ab-b898-4237-961a-ffea7e3a3623 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:ddc58218-832d-4c77-a530-daa7bfd9b73a + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:ec327990-5589-464c-b536-900de7a06189 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:1275731d-9a4b-4574-ba44-22be7740b3ff + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:bf3f3adb-2d1a-428e-9513-1f584d22c6dd + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:4ebb84b7-c911-4fd3-a69b-36b807babf97 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f6a59ad7-149a-4f89-863a-7f0e135fd04a + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:e1ca31f8-6836-4955-9f68-a9f315a16552 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:a8cde33e-b56e-44de-9f37-34e39c1718b7 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:21a2b2be-515d-4fbe-a41d-624aff4f8a38 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:657ad6ac-4500-4f27-abc6-72deb60d1675 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:b4ef37eb-319f-4e9a-aee7-a617a3ff1ce8 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c612cec1-0592-4304-98a8-58f8a925216c + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:602148a4-f4b9-40af-bfab-75228be3ae36 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:94700929-aa94-4ef7-a6a9-0b295b54ddfa + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_01AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:94afd1d3-9540-489e-b0b7-fc2da34d0417 + ecosystem_type: Plant-associated + collection_date: '2016-08-01' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:824f96a7-9df4-41c9-85e1-a4cea1523f59 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:b78f7d73-16a4-4f6c-9bb8-94007fc35202 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f5d1d97c-0484-48d3-9587-bb448da158ae + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:4abe1bdf-5f43-4dd0-91a3-586c062e43e7 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:5d2be109-289c-46cb-9c16-98cc00e6d157 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:60a1ac7b-632d-4295-a80a-b8175656e00c + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:32a3d469-8a93-4fd6-9fe0-16f9ce0132cf + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:78d957a6-d27e-47ec-beb6-86d7420dad3d + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:40539389-eb75-4b1c-9897-2e6f32855a08 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:08251a0c-f982-4ec6-8c0b-bb0177f3410b + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:862b862b-e694-4348-a4ba-3b434b67440a + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:b78cf581-f8e9-4194-aaa4-7062d35298d5 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:53d7d022-896b-4803-b5fc-4003bc023af8 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:63a6d110-3766-4e21-ac0b-62d613c36152 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:ec6a2efb-da59-4b56-98bb-3705b73d3474 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_22AUG2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f5faf681-beb8-4d82-b036-22ca261381b1 + ecosystem_type: Plant-associated + collection_date: '2016-08-22' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:0a7ccc91-f79d-4ef6-b625-20ee412ca032 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:7ec7a3d2-60ac-4c43-829e-a2459351eaf8 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:86598228-4d5d-44c1-8a20-c2b384b2d6d1 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f18cbbaa-2f56-492f-8b1e-ab79c76b4d83 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:e2dcb077-16e1-4540-a7a3-261c9492e60c + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:1eadb7fb-7168-4b37-a018-8b7928316726 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:17679294-55de-4b9b-86da-9fe3d9fdb890 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:6aa94584-37ae-42cc-af29-31ccd73b56bd + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:e7b25f00-b6b2-4d22-8c4a-f608fd5474f7 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:862a50b3-5d7a-4065-bf3d-6e423b055c99 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:a4ad7b54-56fe-49dd-a09d-1a2b369b4f5f + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f2e320bd-7868-453d-9850-234c47b72719 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f6ca2bc7-5573-4512-9bf5-fb389fcbb8ef + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:4954c20b-a444-4649-88f8-9e399143d3f5 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:fa0e2a99-040d-4ec6-be7a-fe6d8ba90c5d + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_12SEP2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c8270368-e522-483f-8190-8c302bcaa140 + ecosystem_type: Plant-associated + collection_date: '2016-09-12' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:132e3aec-eb1a-438d-bcbc-ca4511fdf2a8 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:ad43ccc5-c709-4dac-b598-be10a5bb4217 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:a94c0efe-e560-4524-b5d7-8ac1d7a8a153 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c262276b-9011-4a02-8971-ec137979ebf7 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d53f3e07-9ad2-42a9-ae39-d920129112ac + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f27f0840-4aff-4d94-93b5-e2b30b434927 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:df66adfe-09fe-471c-a900-f3b208341da7 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:b334ad62-f5dc-48d3-b7f0-b89788581244 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:cbb88571-b9a9-4876-ad35-ba0b82b41c0d + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:ee7f1272-14ff-4c20-bed2-dc5528d4f39d + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:451aad09-d814-4e69-b384-c43aa45e480d + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:2c9efdf4-68c3-4085-98a4-2c9efc52d1ef + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:5f524de7-39f2-4573-b42d-e95c60038304 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:49d025c5-94c3-483b-8004-de6a24a63e68 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:bdf36513-e117-4b18-9847-1207e0b35fd5 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_03OCT2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:3af2c3f9-5822-4d57-8eea-4cf4f3144219 + ecosystem_type: Plant-associated + collection_date: '2016-10-03' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_MAIN_07NOV2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d71ed350-917a-4a5b-9c4f-e491ad5df486 + ecosystem_type: Plant-associated + collection_date: '2016-11-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_MAIN_07NOV2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:b0226577-426e-47a0-a57a-14a4b8cb35b5 + ecosystem_type: Plant-associated + collection_date: '2016-11-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_MAIN_07NOV2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:5e45f92d-cb69-4059-be53-09074642e9ab + ecosystem_type: Plant-associated + collection_date: '2016-11-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_MAIN_07NOV2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:423d877e-f692-447f-852b-ca476101c2cd + ecosystem_type: Plant-associated + collection_date: '2016-11-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R1_NF_07NOV2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:bcdd3bb7-f1f3-4336-b7da-0d2153af08f2 + ecosystem_type: Plant-associated + collection_date: '2016-11-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R2_NF_07NOV2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:ce222def-a322-4cd0-9add-618f5abe4688 + ecosystem_type: Plant-associated + collection_date: '2016-11-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R3_NF_07NOV2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:b4a4262e-17fc-4d41-aa7c-c55727a74b25 + ecosystem_type: Plant-associated + collection_date: '2016-11-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G6R4_NF_07NOV2016" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:bd23a3e1-2fee-4023-834a-e4cb9a0571a1 + ecosystem_type: Plant-associated + collection_date: '2016-11-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_15MAY2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:037b5f89-42e7-480a-82b9-4b3586890e28 + ecosystem_type: Plant-associated + collection_date: '2017-05-15' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_15MAY2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:294adf08-906c-415c-a21e-372facfbda5a + ecosystem_type: Plant-associated + collection_date: '2017-05-15' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_15MAY2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:ce94a886-65a2-4c9e-8c65-5a6711ec4551 + ecosystem_type: Plant-associated + collection_date: '2017-05-15' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_15MAY2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:5ecc51f9-94a5-4b27-8ef9-27a59d6e8524 + ecosystem_type: Plant-associated + collection_date: '2017-05-15' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_15MAY2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:1fa7ea40-2cf7-49ff-8478-f32239c95f70 + ecosystem_type: Plant-associated + collection_date: '2017-05-15' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_15MAY2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:5cc6cfa9-7087-4c52-a11c-70e23b78f4aa + ecosystem_type: Plant-associated + collection_date: '2017-05-15' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_15MAY2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:59981b52-c78c-465d-ac28-540d16892cc0 + ecosystem_type: Plant-associated + collection_date: '2017-05-15' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_15MAY2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c9ce3883-2df1-42dd-bee0-4f5edff4918d + ecosystem_type: Plant-associated + collection_date: '2017-05-15' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_05JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c8ed3ef9-c883-423c-8f86-03a21ede6ad8 + ecosystem_type: Plant-associated + collection_date: '2017-06-05' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_05JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:cd66a0eb-dee0-4f6e-b58a-08f0b3d83516 + ecosystem_type: Plant-associated + collection_date: '2017-06-05' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_05JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:e865149e-3a15-4ad3-b167-c223dca36dd4 + ecosystem_type: Plant-associated + collection_date: '2017-06-05' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_05JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:84fd3d6d-6dd9-4a08-a775-794c3a674f5b + ecosystem_type: Plant-associated + collection_date: '2017-06-05' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_05JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:7a9060c2-4fc0-46e4-90d0-e22a188d7a85 + ecosystem_type: Plant-associated + collection_date: '2017-06-05' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_05JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c3e49782-a386-4385-8afc-d32cf66f7b1d + ecosystem_type: Plant-associated + collection_date: '2017-06-05' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_05JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:a4179193-38b5-4aa2-9285-ed8486481ded + ecosystem_type: Plant-associated + collection_date: '2017-06-05' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_05JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:14c783d2-e362-4714-b9c0-82d543416638 + ecosystem_type: Plant-associated + collection_date: '2017-06-05' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_26JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:9c3a480b-4fd0-4da8-823b-8b8a62481511 + ecosystem_type: Plant-associated + collection_date: '2017-06-26' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_26JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:a64ab1e2-b9f2-4fb6-8c7d-4b5804daf2c7 + ecosystem_type: Plant-associated + collection_date: '2017-06-26' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_26JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c961d29c-9cbf-40ff-8e76-7d71b305e77a + ecosystem_type: Plant-associated + collection_date: '2017-06-26' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_26JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:bf9fdb1e-dc32-4ab0-a21e-dcdce379a46d + ecosystem_type: Plant-associated + collection_date: '2017-06-26' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_26JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:51b34532-a300-4936-a3a6-78a004833c10 + ecosystem_type: Plant-associated + collection_date: '2017-06-26' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_26JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:5e16e42e-fa44-4886-99a2-0327ee277102 + ecosystem_type: Plant-associated + collection_date: '2017-06-26' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_26JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:53d81d4e-31cf-40ae-afbc-7db4e5b6ec45 + ecosystem_type: Plant-associated + collection_date: '2017-06-26' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_26JUN2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:aaababfe-dbd3-4df4-b5e8-c774025756e9 + ecosystem_type: Plant-associated + collection_date: '2017-06-26' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_17JUL2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:70710e82-977d-4eb6-9ff9-824b48868741 + ecosystem_type: Plant-associated + collection_date: '2017-07-17' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_17JUL2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f5a9b5a6-7656-4e73-a5a0-c1260a456529 + ecosystem_type: Plant-associated + collection_date: '2017-07-17' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_17JUL2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:0c78fda3-1424-4f6c-b4a9-9e07a84713f1 + ecosystem_type: Plant-associated + collection_date: '2017-07-17' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_17JUL2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:74de6a27-6271-4338-a246-a51167fb6cd7 + ecosystem_type: Plant-associated + collection_date: '2017-07-17' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_17JUL2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:fc666344-9d65-40f7-926e-d0f3e4056f69 + ecosystem_type: Plant-associated + collection_date: '2017-07-17' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_17JUL2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:48f196f0-9267-42f7-b8ea-343b60b3b4c9 + ecosystem_type: Plant-associated + collection_date: '2017-07-17' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_17JUL2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:4ede3f5e-419c-40e5-a38d-a525a212a918 + ecosystem_type: Plant-associated + collection_date: '2017-07-17' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_17JUL2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:ef6c2246-3fd2-46ca-a744-00ca32d5287a + ecosystem_type: Plant-associated + collection_date: '2017-07-17' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_07AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:f2b2ff60-2cdd-4dba-9a3b-1d903a206ca8 + ecosystem_type: Plant-associated + collection_date: '2017-08-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_07AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:c0754834-384e-4282-a75c-39728ec343b8 + ecosystem_type: Plant-associated + collection_date: '2017-08-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_07AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:99757397-ff6e-4a92-b9ee-6b448a9a944d + ecosystem_type: Plant-associated + collection_date: '2017-08-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_07AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:9cc79dd8-95ef-4e8d-aade-6c9ac2216956 + ecosystem_type: Plant-associated + collection_date: '2017-08-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_07AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d34b5892-b5a2-4392-83f5-53ea1abde7dd + ecosystem_type: Plant-associated + collection_date: '2017-08-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_07AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:41240494-f7e0-4f80-a417-93dfdc094a06 + ecosystem_type: Plant-associated + collection_date: '2017-08-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_07AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d191dfe3-3845-455c-bfe1-665dbb7c5e8e + ecosystem_type: Plant-associated + collection_date: '2017-08-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_07AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:2ebb7684-ad20-41b0-b7be-ccf7c7210a13 + ecosystem_type: Plant-associated + collection_date: '2017-08-07' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_28AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:cb03f98b-1929-426a-b4e8-75c0b7f1208b + ecosystem_type: Plant-associated + collection_date: '2017-08-28' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_MAIN_28AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:bee8b493-f526-4a8a-be59-f93e468a2618 + ecosystem_type: Plant-associated + collection_date: '2017-08-28' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_MAIN_28AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:3e2bed09-0d41-4e67-bf73-008a6b3b1073 + ecosystem_type: Plant-associated + collection_date: '2017-08-28' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_MAIN_28AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:451b29e2-f2b3-42f8-adfa-3d8e23ad8545 + ecosystem_type: Plant-associated + collection_date: '2017-08-28' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_NF_28AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:8e985015-830a-4847-bc78-7723772a45d1 + ecosystem_type: Plant-associated + collection_date: '2017-08-28' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R2_NF_28AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:8fb00ba7-a382-4df2-a1b7-eecd087e000a + ecosystem_type: Plant-associated + collection_date: '2017-08-28' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R3_NF_28AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:dfee9c57-72a0-4a4d-8df3-743c1c8eb3e4 + ecosystem_type: Plant-associated + collection_date: '2017-08-28' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R4_NF_28AUG2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:bafedf91-1740-4efe-a542-40f259d68419 + ecosystem_type: Plant-associated + collection_date: '2017-08-28' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - elev: 286 + depth: '0' + lat_lon: 42.39 -85.37 + ecosystem: Environmental + samp_name: "G5R1_MAIN_18SEP2017" + env_medium: plant-associated biome [ENVO:01001001] + env_package: soil + geo_loc_name: 'USA: Kellogg Biological Station, Michigan' + growth_facil: field + analysis_type: + - metagenomics + source_mat_id: UUID:d3f9dcb9-4f7a-4d7b-8ee7-2fa9447f210d + ecosystem_type: Plant-associated + collection_date: '2017-09-18' + env_broad_scale: agricultural biome [ENVO:01001442] + env_local_scale: phyllosphere biome [ENVO:01001442] + samp_store_temp: "-80 Celsius" + ecosystem_subtype: Leaf + ecosystem_category: Terrestrial + specific_ecosystem: Phyllosphere + - 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metagenomics + - id: fake:d4ea2474-11f6-417a-a490-f3688e17437b + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R4_MAIN_28AUG2017 + collection_date: + has_raw_value: '2017-08-28' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:451b29e2-f2b3-42f8-adfa-3d8e23ad8545 + analysis_type: + - 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metagenomics + - id: fake:8f320108-dc67-4eb3-819a-7db6b01bee79 + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R2_NF_28AUG2017 + collection_date: + has_raw_value: '2017-08-28' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:8fb00ba7-a382-4df2-a1b7-eecd087e000a + analysis_type: + - 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metagenomics + - id: fake:5ef661dc-c225-4b49-af33-bec67ba8e1c8 + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R1_MAIN_18SEP2017 + collection_date: + has_raw_value: '2017-09-18' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:d3f9dcb9-4f7a-4d7b-8ee7-2fa9447f210d + analysis_type: + - 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metagenomics + - id: fake:5fa1ea5b-6e47-4bf9-a6c4-c4b6fe48dd1a + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R3_MAIN_18SEP2017 + collection_date: + has_raw_value: '2017-09-18' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:fe48a1cc-4184-467b-ae68-5f599c00327b + analysis_type: + - metagenomics + - id: fake:7ae74a1e-7227-48ee-bebe-2fedf4567f3a + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R4_MAIN_18SEP2017 + collection_date: + has_raw_value: '2017-09-18' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:ac03bdb2-f5b4-4131-9a9a-6d27e7100f55 + analysis_type: + - metagenomics + - id: fake:1cae62f9-6376-4376-baef-faff90d49e38 + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R1_NF_18SEP2017 + collection_date: + has_raw_value: '2017-09-18' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:b2890880-d327-4cc3-91eb-5d06f3cad19d + analysis_type: + - metagenomics + - id: fake:ac66804f-7c3b-4084-af00-17785164e4f3 + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R2_NF_18SEP2017 + collection_date: + has_raw_value: '2017-09-18' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:202eb34b-4d7f-4157-a190-035a4dd907e0 + analysis_type: + - metagenomics + - id: fake:3ad2f76e-fb0c-43c5-8a68-174333b9532d + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R3_NF_18SEP2017 + collection_date: + has_raw_value: '2017-09-18' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:178856e7-f799-4f61-a356-d5d2bd098daa + analysis_type: + - metagenomics + - id: fake:1c2eccb2-5d07-4bf3-8b02-618801211dd2 + part_of: + - fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + env_broad_scale: + has_raw_value: agricultural biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: agricultural biome + env_local_scale: + has_raw_value: phyllosphere biome [ENVO:01001442] + term: + id: ENVO:01001442 + name: phyllosphere biome + env_medium: + has_raw_value: plant-associated biome [ENVO:01001001] + term: + id: ENVO:01001001 + name: plant-associated biome + samp_name: G5R4_NF_18SEP2017 + collection_date: + has_raw_value: '2017-09-18' + depth: + has_raw_value: '0' + has_numeric_value: 0.0 + elev: 286.0 + env_package: + has_raw_value: soil + geo_loc_name: + has_raw_value: 'USA: Kellogg Biological Station, Michigan' + lat_lon: + has_raw_value: 42.39 -85.37 + latitude: 42.39 + longitude: -85.37 + samp_store_temp: + has_raw_value: -80 Celsius + has_unit: Celsius + has_numeric_value: -80.0 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_type: Plant-associated + ecosystem_subtype: Leaf + specific_ecosystem: Phyllosphere + growth_facil: + has_raw_value: field + source_mat_id: + has_raw_value: UUID:4720b174-508e-4b35-875f-373fe661a73a + analysis_type: + - metagenomics + study_set: + - id: fake:d862c2e3-6b0a-42f7-827c-67ebc8d44df7 + name: Seasonal activities of the phyllosphere microbiome of perennial crops + description: Understanding the interactions between plants and microorganisms can + inform microbiome management to enhance crop productivity and resilience to stress. + Here, we apply a genome-centric approach to identify ecologically important leaf + microbiome members on replicated plots of field-grown switchgrass and miscanthus, + and to quantify their activities over two growing seasons for switchgrass. We + use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality + metagenome-assembled-genomes (MAGs). We find that classes represented by these + MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active + in the late season, and upregulate transcripts for short-chain dehydrogenase, + molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways + are expressed for most MAGs, suggesting engagement with the host environment. + We also detect seasonally activated biosynthetic pathways for terpenes and various + non-ribosomal peptide pathways that are poorly annotated. Our findings support + that leaf-associated bacterial populations are seasonally dynamic and responsive + to host cues. + principal_investigator: + orcid: 0000-0002-7189-3067 + email: shade.ashley@gmail.com + name: Ashley Shade + doi: + has_raw_value: 10.46936/10.25585/60000818 + title: Seasonal activities of the phyllosphere microbiome of perennial crops + websites: + - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9950430/ + has_credit_associations: + - applies_to_person: + orcid: 0000-0002-7705-343X + name: Adina Howe + applied_roles: + - Writing review and editing + - Visualization + - Writing original draft + - Investigation + - Formal Analysis + - Data curation + - Conceptualization + - Validation + - Supervision + - Project administration + - Methodology + - Resources + - Software + - Principal Investigator + - Funding acquisition diff --git a/tests/test_graphs/test_submission_portal_graphs.py b/tests/test_graphs/test_submission_portal_graphs.py new file mode 100644 index 00000000..f7972a3c --- /dev/null +++ b/tests/test_graphs/test_submission_portal_graphs.py @@ -0,0 +1,130 @@ +import requests_mock + +from nmdc_runtime.site.graphs import ( + translate_metadata_submission_to_nmdc_schema_database, +) +from nmdc_runtime.site.repository import resource_defs + + +MOCK_PORTAL_API_BASE = "http://www.example.com/nmdc-portal-api" +MOCK_PORTAL_SUBMISSION_ID = "test-submission-id" +MOCK_PORTAL_SUBMISSION = { + "id": MOCK_PORTAL_SUBMISSION_ID, + "metadata_submission": { + "packageName": "plant-associated", + "contextForm": {"datasetDoi": "10.12345/10.12345/00000000"}, + "templates": ["plant-associated"], + "studyForm": { + "studyName": "A test submission", + "piName": "Test Testerson", + "piEmail": "test.testerson@example.com", + "piOrcid": "0000-0000-0000-0000", + "linkOutWebpage": ["http://www.example.com/submission-test"], + "description": "This is a test submission", + "contributors": [ + { + "name": "Test Testerson", + "orcid": "0000-0000-0000-0000", + "roles": [ + "Principal Investigator", + ], + }, + ], + "multiOmicsForm": { + "alternativeNames": [], + "studyNumber": "", + "GOLDStudyId": "", + "JGIStudyId": "", + "NCBIBioProjectId": "", + }, + }, + "sampleData": { + "plant_associated_data": [ + { + "elev": "286", + "depth": "0", + "lat_lon": "42.39 -85.37", + "ecosystem": "Environmental", + "samp_name": "G5R1_MAIN_09MAY2016", + "env_medium": "plant-associated biome [ENVO:01001001]", + "env_package": "soil", + "geo_loc_name": "USA: Kellogg Biological Station, Michigan", + "growth_facil": "field", + "analysis_type": [ + "metagenomics", + ], + "source_mat_id": "UUID:e8ed34cc-32f4-4fc5-9b9f-c2699e43163c", + "ecosystem_type": "Plant-associated", + "collection_date": "2016-05-09", + "env_broad_scale": "agricultural biome [ENVO:01001442]", + "env_local_scale": "phyllosphere biome [ENVO:01001442]", + "samp_store_temp": "-80 Celsius", + "ecosystem_subtype": "Leaf", + "ecosystem_category": "Terrestrial", + "specific_ecosystem": "Phyllosphere", + } + ] + }, + }, +} + + +def test_translate_metadata_submission_to_nmdc_schema_database(): + """Smoke test for translate_metadata_submission_to_nmdc_schema_database job""" + + job = translate_metadata_submission_to_nmdc_schema_database.to_job( + resource_defs=resource_defs + ) + run_config = { + "ops": { + "export_json_to_drs": { + "config": {"username": "test"}, + }, + "fetch_nmdc_portal_submission_by_id": { + "config": { + "submission_id": MOCK_PORTAL_SUBMISSION_ID, + } + }, + }, + "resources": { + "mongo": { + "config": { + "dbname": {"env": "MONGO_DBNAME"}, + "host": {"env": "MONGO_HOST"}, + "password": {"env": "MONGO_PASSWORD"}, + "username": {"env": "MONGO_USERNAME"}, + }, + }, + "nmdc_portal_api_client": { + "config": { + "base_url": MOCK_PORTAL_API_BASE, + "session_cookie": "xyz", + } + }, + "runtime_api_site_client": { + "config": { + "base_url": {"env": "API_HOST"}, + "client_id": {"env": "API_SITE_CLIENT_ID"}, + "client_secret": {"env": "API_SITE_CLIENT_SECRET"}, + "site_id": {"env": "API_SITE_ID"}, + } + }, + "runtime_api_user_client": { + "config": { + "base_url": {"env": "API_HOST"}, + "password": {"env": "API_ADMIN_PASS"}, + "username": {"env": "API_ADMIN_USER"}, + } + }, + }, + } + + with requests_mock.mock(real_http=True) as mock: + mock.get( + f"{MOCK_PORTAL_API_BASE}/api/metadata_submission/{MOCK_PORTAL_SUBMISSION_ID}", + json=MOCK_PORTAL_SUBMISSION, + ) + + result = job.execute_in_process(run_config=run_config) + + assert result.success diff --git a/tests/test_ops/test_data_api_ops.py b/tests/test_ops/test_data_api_ops.py new file mode 100644 index 00000000..91a97413 --- /dev/null +++ b/tests/test_ops/test_data_api_ops.py @@ -0,0 +1,36 @@ +import pytest +import requests_mock + +from dagster import build_op_context + +from nmdc_runtime.site.resources import nmdc_portal_api_client_resource +from nmdc_runtime.site.ops import fetch_nmdc_portal_submission_by_id + + +@pytest.fixture +def client_config(): + return {"base_url": "http://example.com/nmdc_portal", "session_cookie": "12345"} + + +@pytest.fixture +def op_context(client_config): + return build_op_context( + resources={ + "nmdc_portal_api_client": nmdc_portal_api_client_resource.configured( + client_config + ) + }, + op_config={"submission_id": "353d751f-cff0-4558-9051-25a87ba00d3f"}, + ) + + +def test_metadata_submission(op_context): + with requests_mock.mock() as mock: + mock.get( + "http://example.com/nmdc_portal/api/metadata_submission/353d751f-cff0-4558-9051-25a87ba00d3f", + json={"id": "353d751f-cff0-4558-9051-25a87ba00d3f"}, + ) + + fetch_nmdc_portal_submission_by_id(op_context) + + assert len(mock.request_history) == 1 diff --git a/util/mongodump-nmdc.sh b/util/mongodump-nmdc.sh index d0d5906c..e80180fa 100755 --- a/util/mongodump-nmdc.sh +++ b/util/mongodump-nmdc.sh @@ -1,6 +1,14 @@ #!/bin/bash # Execute from repo root dir: -# $ ./util/mongodump-nmdc.sh +# $ export $(grep -v '^#' .env.localhost.prod | xargs) +# $ ./util/mongodump-nmdc.sh mongodump -h $MONGO_HOST -u $MONGO_USERNAME -p $MONGO_PASSWORD --authenticationDatabase=admin \ -d $MONGO_DBNAME \ - --gzip -o $HOME/nmdcdb-mongodump/nmdcdb/$(date +"%Y-%m-%dT%H")/ \ No newline at end of file + --gzip -o $HOME/nmdcdb-mongodump/nmdcdb/$(date +"%Y-%m-%dT%H")/ \ + --excludeCollectionsWithPrefix="_runtime" \ + --excludeCollectionsWithPrefix="_tmp" \ + --excludeCollectionsWithPrefix="fs." \ + --excludeCollectionsWithPrefix="ids_" \ + --excludeCollectionsWithPrefix="txn_log" \ + --excludeCollectionsWithPrefix="functional_annotation_agg" \ + --excludeCollectionsWithPrefix="metaproteomics_" \ No newline at end of file diff --git a/util/mongorestore-nmdc.sh b/util/mongorestore-nmdc.sh index 19b3b85d..9f466627 100755 --- a/util/mongorestore-nmdc.sh +++ b/util/mongorestore-nmdc.sh @@ -1,6 +1,7 @@ #!/bin/bash # Execute from repo root dir: -# $ ./util/mongorestore-nmdc.sh +# $ export $(grep -v '^#' .env.localhost | xargs) +# $ ./util/mongorestore-nmdc.sh mongorestore -h $MONGO_HOST -u $MONGO_USERNAME -p $MONGO_PASSWORD --authenticationDatabase=admin \ --gzip --drop \ - $HOME/nmdcdb-mongodump/nmdcdb/2023-05-17T15/ \ No newline at end of file + $HOME/nmdcdb-mongodump/nmdcdb/$(date +"%Y-%m-%dT%H")/ \ No newline at end of file