Merge branch 'master' of github.com:OBOFoundry/OBOFoundry.github.io

docs/ReviewProcessGuidelines.md

@@ -15,15 +15,15 @@ This page deals with policies and guidelines for the process of ontology review,
 
 # How to request an ontology review #
 
-  1. Go to the OBO Foundry Operations Committee [issue tracker](http://code.google.com/p/obo-foundry-operations-committee/issues/list).
+  1. Go to the OBO Foundry Operations Committee [issue tracker](https://github.com/OBOFoundry/OBOFoundry.github.io/issues).
   1. Click on "New issue".
   1. Select the "Review request" template and follow the instructions on the template.
 
 # Ontology review priority #
 
 Ontologies will be reviewed in the order in which the review request is received. If an ontology previously submitted a request for an OBO Foundry review (that is, before this committee was formed), then the date of the original request is used to determine priority.
 
-Any ontology group wanting a review by the Editorial WG must submit a request on the [issue tracker](http://code.google.com/p/obo-foundry-operations-committee/issues/list)
+Any ontology group wanting a review by the Editorial WG must submit a request on the [issue tracker](https://github.com/OBOFoundry/OBOFoundry.github.io/issues)
 
 # Ontology review workflow #
 

ontology/aero.md

@@ -5,6 +5,9 @@ contact:
   email: [email protected]
   label: Melanie Courtot
 description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events
+license:
+  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 domain: health
 homepage: http://purl.obolibrary.org/obo/aero
 products:

ontology/cmo.md

@@ -7,13 +7,13 @@ contact:
 description: Morphological and physiological measurement records generated from clinical and model organism research and health programs.
 domain: clinical
 homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
-page: ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/
+page: ftp://ftp.rgd.mcw.edu/pub/ontology/clinical_measurement/
 products:
   - id: cmo.owl
   - id: cmo.obo
 title: Clinical measurement ontology
 build:
-  source_url: ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo
+  source_url: ftp://ftp.rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo
   method: obo2owl
 publications:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/22654893

ontology/fbbt.md

@@ -16,6 +16,9 @@ taxon:
   id: NCBITaxon:7227
   label: Drosophila
 title: Drosophila gross anatomy
+license:
+  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 build:
   source_url: http://svn.code.sf.net/p/fbbtdv/code/fbbt/releases/fbbt.owl
   method: owl2obo

ontology/fbcv.md

@@ -11,6 +11,9 @@ homepage: http://purl.obolibrary.org/obo/fbcv
 products:
   - id: fbcv.owl
 title: FlyBase Controlled Vocabulary
+license:
+  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 build:
   source_url: http://sourceforge.net/p/fbcv/code-0/HEAD/tree/src/trunk/ontologies/fbcv-edit.obo?format=raw
   method: obo2owl

ontology/fbdv.md

@@ -16,6 +16,9 @@ taxon:
   id: NCBITaxon:7227
   label: Drosophila
 title: Drosophila development
+license:
+  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
 build:
   source_url: http://svn.code.sf.net/p/fbbtdv/code/fbdv/releases/fbdv.obo
   method: obo2owl

ontology/mmo.md

@@ -7,13 +7,13 @@ contact:
 description: "A representation of the variety of methods used to make clinical and phenotype measurements. "
 domain: clinical
 homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
-page: ftp://rgd.mcw.edu/pub/ontology/measurement_method/
+page: ftp://ftp.rgd.mcw.edu/pub/ontology/measurement_method/
 products:
   - id: mmo.owl
   - id: mmo.obo
 title: Measurement method ontology
 build:
-  source_url: ftp://rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo
+  source_url: ftp://ftp.rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo
   method: obo2owl
 publications:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/22654893

ontology/pw.md

@@ -7,13 +7,13 @@ contact:
 description: A controlled vocabulary for annotating gene products to pathways.
 domain: biological process
 homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
-page: ftp://rgd.mcw.edu/pub/data_release/PW_Introduction.doc
+page: ftp://ftp.rgd.mcw.edu/pub/data_release/PW_Introduction.doc
 products:
   - id: pw.owl
   - id: pw.obo
 title: Pathway ontology
 build:
-  source_url: ftp://rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo
+  source_url: ftp://ftp.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo
   method: obo2owl
 publications:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/21478484

ontology/rs.md

@@ -6,7 +6,7 @@ contact:
   label: Rajni Nigam
 description: Ontology of rat strains
 homepage: http://rgd.mcw.edu/rgdweb/search/strains.html
-page: ftp://rgd.mcw.edu/pub/ontology/rat_strain/
+page: ftp://ftp.rgd.mcw.edu/pub/ontology/rat_strain/
 publications:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/24267899
     title: "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD."
@@ -19,7 +19,7 @@ products:
   - id: rs.obo
 title: Rat Strain Ontology
 build:
-  source_url: ftp://rgd.mcw.edu/pub/ontology/rat_strain/rat_strain.obo
+  source_url: ftp://ftp.rgd.mcw.edu/pub/ontology/rat_strain/rat_strain.obo
   method: obo2owl
 taxon:
   id: NCBITaxon:10114

ontology/xco.md

@@ -7,14 +7,14 @@ description: Conditions under which physiological and morphological measurements
 domain: clinical
 homepage:
   - http://rgd.mcw.edu/rgdweb/ontology/search.html
-  - ftp://rgd.mcw.edu/pub/ontology/experimental_condition/
+  - ftp://ftp.rgd.mcw.edu/pub/ontology/experimental_condition/
 id: xco
 products:
   - id: xco.owl
   - id: xco.obo
 title: Experimental condition ontology
 build:
-  source_url: ftp://rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo
+  source_url: ftp://ftp.rgd.mcw.edu/pub/ontology/experimental_condition/experimental_condition.obo
   method: obo2owl
 publications:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/22654893