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ypriverol merged 1 commit into from
Jul 10, 2026
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Update OWL file #195

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38 changes: 38 additions & 0 deletions pride_cv.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -19988,6 +19988,44 @@
<owl:annotatedTarget>value-type:xsd:string</owl:annotatedTarget>
<rdfs:label>The allowed value-type for this CV term</rdfs:label>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0001011 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0001011">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000017"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000458"/>
<obo:IAO_0000115>Report the major environmental system the sample or specimen came from (MIXS:0000012).</obo:IAO_0000115>
<oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
<oboInOwl:id>PRIDE:0001011</oboInOwl:id>
<rdfs:label>broad-scale environmental context</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0001011"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Report the major environmental system the sample or specimen came from (MIXS:0000012).</owl:annotatedTarget>
<oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>

Comment on lines +19994 to +20010

@coderabbitai coderabbitai Bot Jul 7, 2026

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🗄️ Data Integrity & Integration | 🟡 Minor | ⚡ Quick win

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
set -euo pipefail

# Inspect the target region and similar MIXS-derived terms in pride_cv.owl
git ls-files | rg '(^|/)(pride_cv\.owl|pride_cv\.obo)$'
echo '--- target region ---'
sed -n '19970,20040p' pride_cv.owl

echo '--- similar terms with exact synonym / xref patterns ---'
rg -n -C 3 'env_medium|geo_loc_name|samp_collect_method|soil_type|soil_horizon|env_broad_scale|env_local_scale' pride_cv.owl

echo '--- exact synonym axiom patterns ---'
rg -n -C 2 'hasExactSynonym|hasDbXref>GSCMIXS:' pride_cv.owl

Repository: PRIDE-Archive/pride-ontology

Length of output: 50384

🏁 Script executed:

#!/bin/bash
set -euo pipefail

echo '--- pride_cv.obo entries for PRIDE:0001011 / PRIDE:0001012 ---'
rg -n -C 6 '^(id: PRIDE:0001011|id: PRIDE:0001012|name: broad-scale environmental context|name: local environmental context|synonym:|xref:|def:)' pride_cv.obo

echo '--- exact terms env_broad_scale / env_local_scale in pride_cv.obo ---'
rg -n -C 8 'env_broad_scale|env_local_scale|MIXS:0000012|MIXS:0000013|GSCMIXS:0000012|GSCMIXS:0000013' pride_cv.obo

echo '--- nearby source region around PRIDE:0001011 and PRIDE:0001012 ---'
python3 - <<'PY'
from pathlib import Path
text = Path('pride_cv.obo').read_text(errors='replace').splitlines()
targets = ['PRIDE:0001011', 'PRIDE:0001012']
for i,line in enumerate(text):
    if any(t in line for t in targets):
        start=max(0,i-5); end=min(len(text),i+25)
        print(f'\n@@ around line {i+1} @@')
        for j in range(start,end):
            print(f'{j+1}:{text[j]}')
PY

Repository: PRIDE-Archive/pride-ontology

Length of output: 50385

🏁 Script executed:

#!/bin/bash
set -euo pipefail

echo '--- exact OBO blocks for PRIDE:0001011 and PRIDE:0001012 ---'
awk '
  BEGIN{show=0; n=0}
  /^\[Term\]/{show=0}
  /^id: PRIDE:0001011$/ || /^id: PRIDE:0001012$/{show=1; n=0}
  show{print; n++}
  show && n>20{show=0}
' pride_cv.obo

echo '--- exact synonym / xref occurrences near those ids ---'
rg -n -C 4 'PRIDE:0001011|PRIDE:0001012|env_broad_scale|env_local_scale|GSCMIXS:0000012|GSCMIXS:0000013|MIXS:0000012|MIXS:0000013' pride_cv.obo

echo '--- whether any exact synonym axioms exist for these terms in OWL ---'
rg -n -C 2 'PRIDE_0001011|PRIDE_0001012|hasExactSynonym|GSCMIXS:0000012|GSCMIXS:0000013' pride_cv.owl | sed -n '1,120p'

Repository: PRIDE-Archive/pride-ontology

Length of output: 9375

Add the MIXS field-name synonyms for PRIDE:0001011 and PRIDE:0001012.
Both exports omit the standard hasExactSynonym/GSCMIXS pair for env_broad_scale and env_local_scale, unlike the neighboring MIXS-derived terms. Add those annotations to keep field-to-term mapping consistent.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@pride_cv.owl` around lines 19994 - 20010, Add the missing MIXS field-name
synonym annotations for the PRIDE_0001011 and PRIDE_0001012 class entries so
they match the neighboring MIXS-derived terms. Update each owl:Class block to
include the standard hasExactSynonym and GSCMIXS pair for env_broad_scale and
env_local_scale, keeping the annotations consistent with the existing ontology
pattern and locating the changes by the PRIDE_0001011 and PRIDE_0001012 symbols.



<!-- http://purl.obolibrary.org/obo/PRIDE_0001012 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0001012">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000017"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000458"/>
<obo:IAO_0000115>Report the entity or entities which are in the sample or specimen s local vicinity and which you believe have significant causal influences on your sample or specimen (MIXS:0000013).</obo:IAO_0000115>
<oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
<oboInOwl:id>PRIDE:0001012</oboInOwl:id>
<rdfs:label>local environmental context</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0001012"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Report the entity or entities which are in the sample or specimen s local vicinity and which you believe have significant causal influences on your sample or specimen (MIXS:0000013).</owl:annotatedTarget>
<oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>
</rdf:RDF>
Comment on lines +20013 to 20029

@coderabbitai coderabbitai Bot Jul 7, 2026

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🗄️ Data Integrity & Integration | 🟡 Minor | ⚡ Quick win

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
set -euo pipefail

# Inspect the relevant region and the sibling term mentioned in the comment.
file="pride_cv.owl"

echo "== Nearby lines for PRIDE_0001011 and PRIDE_0001012 =="
sed -n '19970,20060p' "$file" | cat -n

echo
echo "== Search for PRIDE_0001011/0001012 axioms and exact synonyms =="
rg -n -C 3 'PRIDE_0001011|PRIDE_0001012|hasExactSynonym|GSCMIXS:0000013|MIXS:0000013' "$file"

Repository: PRIDE-Archive/pride-ontology

Length of output: 50384

🏁 Script executed:

#!/bin/bash
set -euo pipefail

file="pride_cv.owl"

echo "== MIXS-related annotations =="
rg -n -C 2 'GSCMIXS:000001[23]|env_(broad|local)_scale|MIXS:000001[23]|hasExactSynonym' "$file" | sed -n '1,220p'

echo
echo "== PRIDE_0001011/0001012 blocks only =="
sed -n '20000,20040p' "$file" | cat -n

Repository: PRIDE-Archive/pride-ontology

Length of output: 16242

🌐 Web query:

MIXS:0000013 env_local_scale GSCMIXS:0000013

💡 Result:

MIXS:0000013, commonly referred to by its alias env_local_scale, is a standardized term within the Minimum Information about any (x) Sequence (MIxS) reporting framework, which is developed by the Genomics Standards Consortium (GSC) [1][2][3]. The env_local_scale field is used to document the local environmental context of a sample or specimen [1][4]. Specifically, it requires reporters to identify entities in the immediate vicinity of the sample that are believed to have a significant causal influence on its characteristics or composition [5][6]. Key characteristics of this term include: - Purpose: To describe the local environment with a finer spatial grain than the broader environment (env_broad_scale) [5][6]. - Expected Values: It is recommended to use terms from the Environment Ontology (EnvO) [5][2]. For host-associated or plant-associated samples, terms from interoperable OBO Library ontologies (such as UBERON for anatomical sites or the Plant Ontology) are also accepted [2][6]. - Format: The value should generally follow a pattern of a term label and its associated ID, for example, "litter layer [ENVO:01000338]" [2][7]. - Requirement: In the MIxS schema, this is typically a required field for various environmental and biological packages [7][8][9]. The GSC provides guidelines for using EnvO in conjunction with MIxS to ensure consistent and interoperable metadata reporting [5][6].

Citations:

🏁 Script executed:

#!/bin/bash
set -euo pipefail

file="pride_cv.owl"

echo "== Any GSCMIXS annotations in the file =="
rg -n 'GSCMIXS:' "$file" || true

echo
echo "== Any exact synonyms on the MIXS-related block =="
sed -n '20008,20032p' "$file" | rg -n 'hasExactSynonym|hasDbXref|MIXS:0000012|MIXS:0000013|env_broad_scale|env_local_scale'

echo
echo "== Nearby MIXS-related class blocks with annotations, if any =="
rg -n -C 3 'MIXS:0000012|MIXS:0000013|env_broad_scale|env_local_scale|hasExactSynonym|hasDbXref' "$file" | sed -n '1,120p'

Repository: PRIDE-Archive/pride-ontology

Length of output: 7719

Add the MIXS synonym/xref pair for PRIDE:0001012. PRIDE:0001012 maps to env_local_scale (MIXS:0000013), so add the oboInOwl:hasExactSynonym annotation and matching GSCMIXS:0000013 xref axiom here to keep the MIXS terms aligned.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@pride_cv.owl` around lines 20013 - 20029, Add the missing MIXS synonym/xref
pair for PRIDE_0001012 in the PRIDE_0001012 class and its annotation block:
include an oboInOwl:hasExactSynonym for env_local_scale and add the matching
GSCMIXS:0000013 xref in the owl:Axiom alongside the existing IAO_0000115
annotation so the PRIDE and MIXS mappings stay aligned.



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