Update pride_cv.obo

[nithujohn]

User description

Added human gut metaproteomics mixs package
https://genomicsstandardsconsortium.github.io/mixs/0016004/
@ypriverol @deeptijk please have a look and let me know the changes to make as well. Thanks!

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PR Type

Enhancement

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Description

• Added new ontology terms for human gut metaproteomics.

• Introduced 48 new terms under the Human gut category.

• Enhanced metadata coverage for gut microbiome studies.

• Improved compatibility with MIXS standards for metaproteomics.

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Changes walkthrough 📝

	Relevant files
Enhancement	pride_cv.obo Added human gut metaproteomics terms to ontology                  pride_cv.obo Added a new term Human gut as a parent category. Introduced 48 child terms under Human gut for detailed metadata. Enhanced definitions with references to MIXS standards. Improved ontology structure for gut microbiome research. +226/-0

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⚡ Recommended focus areas for review Duplicate Term Terms PRIDE:0000704 and PRIDE:0000705 are identical duplicates with the same name and definition for 'sample volume or weight for DNA extraction' 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 Missing Fields Several terms are missing recommended OBO fields like synonyms, xrefs, and comments that would provide additional context and interoperability [Term] id: PRIDE:0000671 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:0000672 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:0000673 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:0000674 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:0000675 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:0000676 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:0000677 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:0000678 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:0000679 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:0000680 name: IHMC medication code def: "Can include multiple medication codes. MIXS:0000884" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Human gut [Term] id: PRIDE:0000681 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:0000682 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:0000684 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:0000685 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:0000686 name: host height def: "The height of subject. MIXS:0000264" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Human gut [Term] id: PRIDE:0000687 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:0000688 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:0000689 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:0000690 name: host genotype def: "Observed genotype MIXS:0000365" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Human gut [Term] id: PRIDE:0000691 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:0000692 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:0000693 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:0000694 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:0000695 name: host occupation def: "Most frequent job performed by subject. MIXS:0000896" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Human gut [Term] id: PRIDE:0000696 name: medical history performed def: "Whether full medical history was collected. MIXS:0000897" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Human gut [Term] id: PRIDE:0000697 name: host pulse def: "Resting pulse, measured as beats per minutes. MIXS:0000333" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Human gut [Term] id: PRIDE:0000698 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:0000699 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:0000700 name: oxygenation status of sample def: "Oxygenation status of the sample. MIXS:0000753" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Human gut [Term] id: PRIDE:0000701 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:0000702 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:0000703 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:0000704 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: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

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PR Code Suggestions ✨

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Category	Suggestion	Score
Possible issue	✅ Remove duplicate ontology term Suggestion Impact: The commit removed the duplicate definition of PRIDE:0000704 and moved the term definition to PRIDE:0000706 instead code diff: [Term] -id: PRIDE:0000703 +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:0000704 -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 Remove duplicate term definition for 'sample volume or weight for DNA extraction' (PRIDE:0000704 and PRIDE:0000705) as they have identical content. pride_cv.obo [4258-4267] [Term] id: PRIDE:0000704 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: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 - Apply this suggestion Suggestion importance[1-10]: 9 Why: The suggestion identifies a critical issue where identical ontology terms (PRIDE:0000704 and PRIDE:0000705) are duplicated with the same name and definition, which could cause confusion and inconsistency in the ontology structure.	9

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CI Feedback 🧐

(Feedback updated until commit b32e670)

A test triggered by this PR failed. Here is an AI-generated analysis of the failure:

Action: build

Failed stage: Validate OBO file [❌]

Failed test name: fastobo-validator

Failure summary: The action failed because the OBO file validation detected duplicate IDs in the pride_cv.obo file. Specifically, the ID PRIDE:0000672 appears 2 times in the file, which violates the unique identifier requirement for OBO ontologies.

Relevant error logs: 1: ##[group]Operating System 2: Ubuntu ... 374: [command]/usr/bin/git log -1 --format='%H' 375: 'ca244bd4aa45bdcf3aa62e6d5d872ad3d777d598' 376: ##[group]Run fastobo-validator --duplicates pride_cv.obo 377: �[36;1mfastobo-validator --duplicates pride_cv.obo�[0m 378: shell: sh -e {0} 379: ##[endgroup] 380: Parsing `pride_cv.obo` 381: Finished parsing `pride_cv.obo` in 0.00s 382: Failed validation of `pride_cv.obo` (1 errors) 383: --> in complete document 384: id `PRIDE:0000672` appears more than once (2 times) 385: ##[error]Process completed with exit code 1.