Skip to content

Obsolete OBA terms referencing obsoleted PRO entities #406

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 3 commits into
base: master
Choose a base branch
from
Draft

Obsolete OBA terms referencing obsoleted PRO entities #406

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
98556db
Initial plan
Copilot Oct 29, 2025
9336d1e
Initial exploration: understanding obsolete PRO terms issue
Copilot Oct 29, 2025
ab8ca71
Obsolete five OBA terms with obsoleted PRO entities
Copilot Oct 29, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
34 changes: 32 additions & 2 deletions src/ontology/components/obsoletes.owl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/oba/components/obsoletes.owl>
<http://purl.obolibrary.org/obo/oba/releases/2025-07-08/components/obsoletes.owl>
Annotation(owl:versionInfo "2025-07-08")
<http://purl.obolibrary.org/obo/oba/releases/2025-10-29/components/obsoletes.owl>
Annotation(owl:versionInfo "2025-10-29")

Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0000037>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_0000039>))
Expand Down Expand Up @@ -77,7 +77,12 @@ Declaration(Class(<http://purl.obolibrary.org/obo/OBA_1001041>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_1001042>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_1001043>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_1001044>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2043233>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2044443>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2050081>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2058599>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2059278>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_2081815>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0000187>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0002918>))
Declaration(Class(<http://purl.obolibrary.org/obo/OBA_VT0003952>))
Expand Down Expand Up @@ -426,12 +431,37 @@ AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_1001043>
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/OBA_1001044> <http://purl.obolibrary.org/obo/OBA_VT0007031>)
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_1001044> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/OBA_2043233> (<http://purl.obolibrary.org/obo/OBA_2043233>)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2043233> "Reason for obsoletion: The protein entity PR:000013872 (regenerating islet-derived protein 3-gamma) has been obsoleted by the Protein Ontology.")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2043233> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/OBA_2044443> (<http://purl.obolibrary.org/obo/OBA_2044443>)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2044443> "Reason for obsoletion: The protein entity PR:000030596 (putative uncharacterized protein TXNRD3NB) has been obsoleted by the Protein Ontology.")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2044443> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/OBA_2050081> (<http://purl.obolibrary.org/obo/OBA_2050081>)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/OBA_2050081> <http://purl.obolibrary.org/obo/OBA_2045319>)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2050081> "Reason for obsoletion: a term with the same intended meaning already exists.")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2050081> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/OBA_2058599> (<http://purl.obolibrary.org/obo/OBA_2058599>)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2058599> "Reason for obsoletion: The protein entity PR:Q12799 (putative T-complex protein 10A homolog (human)) has been obsoleted by the Protein Ontology.")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2058599> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/OBA_2059278> (<http://purl.obolibrary.org/obo/OBA_2059278>)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2059278> "Reason for obsoletion: The protein entity PR:Q6F5E7 (putative uncharacterized protein TXNRD3NB (human)) has been obsoleted by the Protein Ontology.")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2059278> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/OBA_2081815> (<http://purl.obolibrary.org/obo/OBA_2081815>)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/OBA_2081815> "Reason for obsoletion: The protein entity PR:Q9Y4X1 (UDP-glucuronosyltransferase 2A1 (human)) has been obsoleted by the Protein Ontology.")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/OBA_2081815> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/OBA_VT0000187> (<http://purl.obolibrary.org/obo/OBA_VT0000187>)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/OBA_VT0000187> <http://purl.obolibrary.org/obo/OBA_2040183>)
Expand Down
5 changes: 0 additions & 5 deletions src/patterns/data/default/entity_attribute_location.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3314,7 +3314,6 @@ OBA:2043229 level of receptor expression-enhancing protein 2 in blood serum PR:0
OBA:2043230 level of lithostathine-1-alpha in blood serum PR:000013869 lithostathine-1-alpha PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2043231 level of lithostathine-1-beta in blood serum PR:000013870 lithostathine-1-beta PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2043232 level of regenerating islet-derived protein 3-alpha in blood serum PR:000013871 regenerating islet-derived protein 3-alpha PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2043233 level of regenerating islet-derived protein 3-gamma in blood serum PR:000013872 regenerating islet-derived protein 3-gamma PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2043234 level of transcription factor RelB in blood serum PR:000013876 transcription factor RelB PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2043235 level of RELT-like protein 1 in blood serum PR:000013877 RELT-like protein 1 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2043236 level of RELT-like protein 2 in blood serum PR:000013878 RELT-like protein 2 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
Expand Down Expand Up @@ -4524,7 +4523,6 @@ OBA:2044439 level of protein FAM171A1 in blood serum PR:000030586 protein FAM171
OBA:2044440 level of V-set and immunoglobulin domain-containing protein 8 in blood serum PR:000030592 V-set and immunoglobulin domain-containing protein 8 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2044441 level of protein FAM162B in blood serum PR:000030593 protein FAM162B PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2044442 level of metallophosphoesterase MPPED2 in blood serum PR:000030594 metallophosphoesterase MPPED2 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2044443 level of putative uncharacterized protein TXNRD3NB in blood serum PR:000030596 putative uncharacterized protein TXNRD3NB PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2044444 level of E3 ubiquitin-protein ligase HECTD3 in blood serum PR:000030605 E3 ubiquitin-protein ligase HECTD3 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2044445 level of transmembrane protein 185A in blood serum PR:000030611 transmembrane protein 185A PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
OBA:2044446 level of piezo-type mechanosensitive ion channel component 1 in blood serum PR:000030614 piezo-type mechanosensitive ion channel component 1 PATO:0000070 amount UBERON:0001977 blood serum https://orcid.org/0000-0001-8314-2140
Expand Down Expand Up @@ -11013,7 +11011,6 @@ OBA:2058595 level of twinfilin-1 (human) in cerebrospinal fluid PR:Q12792 twinfi
OBA:2058596 level of hyaluronidase-1 (human) in cerebrospinal fluid PR:Q12794 hyaluronidase-1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2058597 level of aspartyl/asparaginyl beta-hydroxylase (human) in cerebrospinal fluid PR:Q12797 aspartyl/asparaginyl beta-hydroxylase (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2058598 level of centrin-1 (human) in cerebrospinal fluid PR:Q12798 centrin-1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2058599 level of obsolete putative T-complex protein 10A homolog (human) in cerebrospinal fluid PR:Q12799 obsolete putative T-complex protein 10A homolog (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2058600 level of EGF-containing fibulin-like extracellular matrix protein 1 (human) in cerebrospinal fluid PR:Q12805 EGF-containing fibulin-like extracellular matrix protein 1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2058601 level of nucleosome-remodeling factor subunit BPTF (human) in cerebrospinal fluid PR:Q12830 nucleosome-remodeling factor subunit BPTF (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2058602 level of zona pellucida sperm-binding protein 4 (human) in cerebrospinal fluid PR:Q12836 zona pellucida sperm-binding protein 4 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
Expand Down Expand Up @@ -11692,7 +11689,6 @@ OBA:2059274 level of interleukin-31 (human) in cerebrospinal fluid PR:Q6EBC2 int
OBA:2059275 level of small ubiquitin-related modifier 4 (human) in cerebrospinal fluid PR:Q6EEV6 small ubiquitin-related modifier 4 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2059276 level of C-type lectin domain family 6 member A (human) in cerebrospinal fluid PR:Q6EIG7 C-type lectin domain family 6 member A (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2059277 level of vasorin (human) in cerebrospinal fluid PR:Q6EMK4 vasorin (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2059278 level of obsolete putative uncharacterized protein TXNRD3NB (human) in cerebrospinal fluid PR:Q6F5E7 obsolete putative uncharacterized protein TXNRD3NB (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2059279 level of secreted frizzled-related protein 4 (human) in cerebrospinal fluid PR:Q6FHJ7 secreted frizzled-related protein 4 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2059280 level of fatty-acid amide hydrolase 2 (human) in cerebrospinal fluid PR:Q6GMR7 fatty-acid amide hydrolase 2 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2059281 level of putative peptidyl-tRNA hydrolase PTRHD1 (human) in cerebrospinal fluid PR:Q6GMV3 putative peptidyl-tRNA hydrolase PTRHD1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
Expand Down Expand Up @@ -14229,7 +14225,6 @@ OBA:2081811 level of cysteine protease ATG4B (human) in cerebrospinal fluid PR:Q
OBA:2081812 level of transducin beta-like protein 2 (human) in cerebrospinal fluid PR:Q9Y4P3 transducin beta-like protein 2 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2081813 level of sperm flagellar protein 1 (human) in cerebrospinal fluid PR:Q9Y4P9 sperm flagellar protein 1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2081814 level of cyanocobalamin reductase / alkylcobalamin dealkylase (human) in cerebrospinal fluid PR:Q9Y4U1 cyanocobalamin reductase / alkylcobalamin dealkylase (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2081815 level of obsolete UDP-glucuronosyltransferase 2A1 (human) in cerebrospinal fluid PR:Q9Y4X1 obsolete UDP-glucuronosyltransferase 2A1 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2081816 level of C-C motif chemokine 27 (human) in cerebrospinal fluid PR:Q9Y4X3 C-C motif chemokine 27 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2081817 level of U6 snRNA-associated Sm-like protein LSm4 (human) in cerebrospinal fluid PR:Q9Y4Z0 U6 snRNA-associated Sm-like protein LSm4 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
OBA:2081818 level of neurogenin-3 (human) in cerebrospinal fluid PR:Q9Y4Z2 neurogenin-3 (human) PATO:0000070 amount UBERON:0001359 cerebrospinal fluid PMID:39528825 https://orcid.org/0000-0001-6757-4744
Expand Down
Loading
Loading