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Update pride_cv.obo #121

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Update pride_cv.obo #121

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4fce143
Update pride_cv.obo
nithujohn Jan 23, 2025
6260916
Merge branch 'master' into metaproteomics
nithujohn Jan 23, 2025
1caddfe
Update pride_cv.obo
nithujohn Jan 23, 2025
b32e670
Merge branch 'metaproteomics' of https://github.com/PRIDE-Archive/pri…
nithujohn Jan 23, 2025
e540d95
Update pride_cv.obo
nithujohn Jan 23, 2025
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226 changes: 223 additions & 3 deletions pride_cv.obo
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
format-version: 1.4
date: 16:01:2025 14:06
data-version: 2.1.8
saved-by: Deepti Jaiswal Kundu
date: 23:01:2025 14:57
data-version: 2.1.9
saved-by: Nithu Sara John
auto-generated-by: OBO-Edit 2.3.1
default-namespace: PRIDE
remark: I would set treat-xrefs-as-equivalent but there are some weird xrefs that would break that behaviour (PRIDE:PRIDE, value-type:xsd\:string, ...)
Expand Down Expand Up @@ -4075,6 +4075,226 @@ name: Olink Target
def: "Olink Target is a proteomics platform designed for focused, customizable analysis of specific protein biomarker panels using proximity extension assay (PEA) technology." [PRIDE:PRIDE]
is_a: PRIDE:0000654 ! Olink instrument model

[Term]
id: PRIDE:0000673
name: Human gut
def: "A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome." [PRIDE:PRIDE]

[Term]
id: PRIDE:0000674
name: sample name
def: "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. MIXS:0001107" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000675
name: project name
def: "Name of the project within which the sequencing was organized. MIXS:0000092" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000676
name: gastrointestinal tract disorder
def: "History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000677
name: liver disorder
def: "History of liver disorders; can include multiple disorders. MIXS:0000282" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000678
name: special diet
def: "Specification of special diet; can include multiple special diets. MIXS:0000905" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000679
name: host subject id
def: "A unique identifier by which each subject can be referred to, de-identified. MIXS:0000861" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000680
name: host age
def: "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees. MIXS:0000255" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000681
name: host disease status
def: "List of diseases with which the host has been diagnosed; can include multiple diagnoses. MIXS:0000031" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000682
name: IHMC medication code
def: "Can include multiple medication codes. MIXS:0000884" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000683
name: chemical administration
def: "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. MIXS:0000751" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000684
name: host body site
def: "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc.). MIXS:0000867" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000685
name: host body product
def: "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. MIXS:0000888" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000686
name: host total mass
def: "Total mass of the host at collection, the unit depends on host. MIXS:0000263" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000687
name: host height
def: "The height of subject. MIXS:0000264" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000688
name: host diet
def: "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types. MIXS:0000869" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000689
name: host last meal
def: "Content of last meal and time since feeding; can include multiple values. MIXS:0000870" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000690
name: host family relationship
def: "Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000691
name: host genotype
def: "Observed genotype MIXS:0000365" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000692
name: host phenotype
def: "Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000693
name: host body temperature
def: "Core body temperature of the host when sample was collected. MIXS:0000874" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000694
name: host body-mass index
def: "Body mass index, calculated as weight/(height)squared. MIXS:0000317" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000695
name: ethnicity
def: "A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. MIXS:0000895" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000696
name: host occupation
def: "Most frequent job performed by subject. MIXS:0000896" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000697
name: medical history performed
def: "Whether full medical history was collected. MIXS:0000897" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000698
name: host pulse
def: "Resting pulse, measured as beats per minutes. MIXS:0000333" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000699
name: perturbation
def: "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types. MIXS:0000754" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000700
name: salinity
def: "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater. MIXS:0000183" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000701
name: oxygenation status of sample
def: "Oxygenation status of the sample. MIXS:0000753" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000702
name: temperature
def: "Temperature of the sample at the time of sampling. MIXS:0000113" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000703
name: organism count
def: "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr). MIXS:0000103" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000704
name: sample storage temperature
def: "Temperature at which sample was stored, e.g. -80 degree Celsius. MIXS:0000110" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000705
name: sample volume or weight for DNA extraction
def: "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001). MIXS:0000111" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000706
name: sample storage duration
def: "Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. MIXS:0000116" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000707
name: observed host symbionts
def: "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite). MIXS:0001298" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000708
name: sample storage location
def: "Location at which sample was stored, usually name of a specific freezer/room. MIXS:0000755" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Term]
id: PRIDE:0000709
name: miscellaneous parameter
def: "Any other measurement performed or parameter collected, that is not listed here. MIXS:0000752" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Human gut

[Typedef]
id: http://purl.obolibrary.org/obo/PRIDE_part_of
Expand Down
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