# ARO -> GO mapping (SSSOM) # # CARD/ARO carries no native GO cross-references (verified against aro.owl: hasDbXref # namespaces are ARO/PMID/PubChem/ChEBI/ChEMBL/CAS/PDB/ISBN/RO/DOID, zero GO). This file is the # hand-curated ARO->GO bridge described in projects/ANTIMICROBIAL_RESISTANCE.md, seeded from the # macrolide phosphotransferase (MPH) family. # # Every entity is given as a CURIE + label tuple (subject_id/subject_label, # predicate_id/predicate_label, object_id/object_label) so the rows are self-describing. # # Validate with linkml-validate (ltv) -- either via the just recipe: # just validate-mappings # or directly (schema ships with the sssom_schema pip package): # uv run linkml-validate \ # -s "$(uv run python -c 'import sssom_schema,os;print(os.path.join(os.path.dirname(sssom_schema.__file__),"schema","sssom_schema.yaml"))')" \ # -C "mapping set" projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml mapping_set_id: https://w3id.org/ai4curation/ai-gene-review/mappings/aro2go mapping_set_title: ARO to GO mapping (AMR gene families and resistance mechanisms) mapping_set_description: >- Curated mappings from Antibiotic Resistance Ontology (ARO / CARD) determinant, AMR-gene-family, and resistance-mechanism terms to Gene Ontology molecular-function and biological-process terms. CARD provides no native ARO->GO cross-references, so these are manually asserted to seed and quality-check GO annotations of AMR genes (e.g. MphA Q47396 / ARO:3000316, MphB A0A0H3EUF3 / ARO:3000318). Coverage: the macrolide phosphotransferase (MPH) family plus beta-lactamase, chloramphenicol acetyltransferase, aminoglycoside-modifying enzymes (APH/AAC/ANT), Erm rRNA methyltransferases, trimethoprim-resistant DHFR and sulfonamide-resistant DHPS, and the six ARO resistance-mechanism classes. Every ARO id is verified against aro.owl; every GO id/label against QuickGO. Gene/family -> MF use 'enables' (RO:0002327); mechanism -> BP use skos:relatedMatch. license: https://creativecommons.org/licenses/by/4.0/ creator_label: - AI Gene Review project mapping_date: "2026-06-12" curie_map: ARO: http://purl.obolibrary.org/obo/ARO_ GO: http://purl.obolibrary.org/obo/GO_ RO: http://purl.obolibrary.org/obo/RO_ skos: http://www.w3.org/2004/02/skos/core# semapv: https://w3id.org/semapv/vocab/ sssom: https://w3id.org/sssom/ obo: http://purl.obolibrary.org/obo/ mappings: # --- Determinant (gene) -> molecular function --- - subject_id: ARO:3000316 subject_label: mphA predicate_id: RO:0002327 predicate_label: enables object_id: GO:0050073 object_label: macrolide 2'-kinase activity mapping_justification: semapv:ManualMappingCuration comment: >- mph(A) / macrolide 2'-phosphotransferase I enables the GO macrolide 2'-kinase activity (the determinant is not a GO term, so this is an enables relation, not a term equivalence). - subject_id: ARO:3000318 subject_label: mphB predicate_id: RO:0002327 predicate_label: enables object_id: GO:0050073 object_label: macrolide 2'-kinase activity mapping_justification: semapv:ManualMappingCuration comment: >- mph(B) / macrolide 2'-phosphotransferase II enables the same GO MF; substrate-scope differences (16-membered macrolides) are finer than the GO term and recorded separately as ChEBI substrates. # --- AMR gene family -> molecular function --- - subject_id: ARO:3000333 subject_label: macrolide phosphotransferase (MPH) predicate_id: RO:0002327 predicate_label: enables object_id: GO:0050073 object_label: macrolide 2'-kinase activity mapping_justification: semapv:ManualMappingCuration comment: >- Family-level mapping: every member of the ARO macrolide phosphotransferase (MPH) family is a macrolide 2'-kinase. Useful for propagating a candidate GO MF to other MPH members (mphC/E/G). # --- Resistance mechanism -> biological process --- - subject_id: ARO:0001004 subject_label: antibiotic inactivation predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0046677 object_label: response to antibiotic mapping_justification: semapv:ManualMappingCuration comment: >- Mechanism axis (ARO 'antibiotic inactivation') relates to the GO biological process 'response to antibiotic'; relatedMatch (not exact) because the two terms sit on different axes. This row is the mechanism->BP QC prior: an inactivation-mechanism determinant should carry GO:0046677. # --- Other resistance mechanisms -> biological process --- # All ARO mechanism-axis terms relate to GO:0046677 'response to antibiotic' (relatedMatch; the BP an # AMR determinant participates in, regardless of the specific mechanism). Verified ARO ids from aro.owl. - subject_id: ARO:0010000 subject_label: antibiotic efflux predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0046677 object_label: response to antibiotic mapping_justification: semapv:ManualMappingCuration comment: >- Efflux determinants additionally have a transmembrane-transporter MF, but GO lacks a specific 'antibiotic/efflux transmembrane transporter activity' term, so only the BP prior is asserted here. - subject_id: ARO:0001001 subject_label: antibiotic target alteration predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0046677 object_label: response to antibiotic mapping_justification: semapv:ManualMappingCuration - subject_id: ARO:0001003 subject_label: antibiotic target protection predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0046677 object_label: response to antibiotic mapping_justification: semapv:ManualMappingCuration - subject_id: ARO:0001002 subject_label: antibiotic target replacement predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0046677 object_label: response to antibiotic mapping_justification: semapv:ManualMappingCuration - subject_id: ARO:3000244 subject_label: reduced permeability to antibiotic predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0046677 object_label: response to antibiotic mapping_justification: semapv:ManualMappingCuration # --- Other AMR gene families -> molecular function (enables) --- # Family-level 'enables' mappings: every member of the ARO family carries the named GO MF. Useful for # propagating a candidate GO MF to family members. Verified: ARO ids from aro.owl, GO ids/labels from QuickGO. - subject_id: ARO:3000001 subject_label: beta-lactamase predicate_id: RO:0002327 predicate_label: enables object_id: GO:0008800 object_label: beta-lactamase activity mapping_justification: semapv:ManualMappingCuration - subject_id: ARO:3000122 subject_label: chloramphenicol acetyltransferase (CAT) predicate_id: RO:0002327 predicate_label: enables object_id: GO:0008811 object_label: chloramphenicol O-acetyltransferase activity mapping_justification: semapv:ManualMappingCuration - subject_id: ARO:3000114 subject_label: aminoglycoside phosphotransferase (APH) predicate_id: RO:0002327 predicate_label: enables object_id: GO:0034071 object_label: aminoglycoside phosphotransferase activity mapping_justification: semapv:ManualMappingCuration - subject_id: ARO:3000121 subject_label: aminoglycoside acetyltransferase (AAC) predicate_id: RO:0002327 predicate_label: enables object_id: GO:0034069 object_label: aminoglycoside N-acetyltransferase activity mapping_justification: semapv:ManualMappingCuration - subject_id: ARO:3000218 subject_label: aminoglycoside nucleotidyltransferase (ANT) predicate_id: RO:0002327 predicate_label: enables object_id: GO:0034068 object_label: aminoglycoside nucleotidyltransferase activity mapping_justification: semapv:ManualMappingCuration - subject_id: ARO:3000560 subject_label: Erm 23S ribosomal RNA methyltransferase predicate_id: RO:0002327 predicate_label: enables object_id: GO:0008988 object_label: rRNA (adenine-N6-)-methyltransferase activity mapping_justification: semapv:ManualMappingCuration comment: >- Family-safe term: all Erm methylate the N6 of 23S rRNA adenine A2058, so every member enables GO:0008988 (rRNA adenine-N6-methyltransferase). The N6,N6-DImethyltransferase term GO:0052910 (a descendant of GO:0008988) is correct only for the di-methylating majority and would over-annotate mono-methylating Erm variants, so it is applied at the allele level, not the family node. - subject_id: ARO:3001218 subject_label: trimethoprim resistant dihydrofolate reductase dfr predicate_id: RO:0002327 predicate_label: enables object_id: GO:0004146 object_label: dihydrofolate reductase activity mapping_justification: semapv:ManualMappingCuration comment: >- Target-replacement resistance: a drug-insensitive Dfr variant that retains dihydrofolate reductase activity (the resistance is to trimethoprim, not loss of the GO MF). - subject_id: ARO:3003415 subject_label: sulfonamide resistant dihydropteroate synthase folP predicate_id: RO:0002327 predicate_label: enables object_id: GO:0004156 object_label: dihydropteroate synthase activity mapping_justification: semapv:ManualMappingCuration comment: >- Target-replacement resistance: a sulfonamide-insensitive Sul/FolP variant that retains dihydropteroate synthase activity. - subject_id: ARO:3000149 subject_label: FosA predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0004364 object_label: glutathione transferase activity mapping_justification: semapv:ManualMappingCuration comment: >- Re-anchored from the heterogeneous parent ARO:3000133 'fosfomycin thiol transferase' to the glutathione-specific FosA: FosA adds glutathione to fosfomycin's epoxide and genuinely has GST activity. The parent node also contains FosB (bacillithiol/L-cysteine thiol transferase, NOT glutathione) and FosX (an epoxide hydrolase), for which GO:0004364 would be wrong. relatedMatch because GO:0004364 is the general GST activity (no fosfomycin-specific term; GO:0034797/0034798 are obsolete). The other FosA-type GSTs (FosA2/FosA3/fosA5) are ARO siblings (not descendants) and are mapped separately below; FosB/FosX are deliberately excluded. - subject_id: ARO:3002804 subject_label: FosA2 predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0004364 object_label: glutathione transferase activity mapping_justification: semapv:ManualMappingCuration comment: >- FosA-type Mn2+/K+-dependent glutathione S-transferase (chromosomal FosA of Enterobacter cloacae); same fosfomycin-GSH conjugation activity as FosA. relatedMatch to the general GST term. - subject_id: ARO:3002872 subject_label: FosA3 predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0004364 object_label: glutathione transferase activity mapping_justification: semapv:ManualMappingCuration comment: >- FosA-type glutathione S-transferase; the most widespread plasmid-borne FosA in ESBL-producing Enterobacterales. relatedMatch to the general GST term. - subject_id: ARO:3003209 subject_label: fosA5 predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0004364 object_label: glutathione transferase activity mapping_justification: semapv:ManualMappingCuration comment: >- FosA-type glutathione S-transferase (K. pneumoniae origin); same fosfomycin-GSH conjugation activity. relatedMatch to the general GST term. - subject_id: ARO:3004112 subject_label: phosphoethanolamine transferase conferring colistin resistance predicate_id: RO:0002327 predicate_label: enables object_id: GO:0043838 object_label: phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity mapping_justification: semapv:ManualMappingCuration comment: >- Colistin resistance (last-resort): MCR/EptA-type enzymes transfer phosphoethanolamine onto lipid A, reducing the net negative charge that polymyxins bind. This ARO family node covers the mobile MCR alleles plus pmr and intrinsic chromosomal phosphoethanolamine transferases (>110 descendant ARO terms), all of which enable this exact GO MF. - subject_id: ARO:3004271 subject_label: 16S rRNA methyltransferase (G1405) predicate_id: skos:relatedMatch predicate_label: related match object_id: GO:0070043 object_label: rRNA (guanine-N7-)-methyltransferase activity mapping_justification: semapv:ManualMappingCuration comment: >- High-level aminoglycoside resistance: ArmA/RmtA-H-type 16S rRNA methyltransferases methylate N7 of G1405 in the aminoglycoside binding site. relatedMatch (not enables) because GO:0070043 is the general rRNA guanine-N7-methyltransferase activity (which also covers housekeeping enzymes such as RsmG); the G1405-specific resistance methyltransferase is narrower than this term, so the GO MF still propagates. # --- Gaps: ARO families with NO suitable GO molecular-function term --- # Recorded with the SSSOM no-match convention (object_id: sssom:NoTermFound, object_source: obo:go.owl) # so the gap lives in the mapping file itself rather than only in prose. These are candidates for GO # new-term requests. predicate_id is the relation we WOULD use (skos:exactMatch) had a term existed. - subject_id: ARO:3000221 subject_label: lincosamide nucleotidyltransferase (LNU) predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- GO has no lincosamide (O-)nucleotidyltransferase MF term (Lnu adenylylates lincosamides). GO term request candidate. - subject_id: ARO:3000453 subject_label: streptogramin vat acetyltransferase predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- GO has no streptogramin A O-acetyltransferase MF term (Vat). GO term request candidate. - subject_id: ARO:3000376 subject_label: streptogramin vgb lyase predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- GO has no streptogramin B (virginiamycin B) lyase MF term (Vgb). GO term request candidate. - subject_id: ARO:3000320 subject_label: macrolide esterase predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- GO has no macrolide/erythromycin esterase MF term (Ere). GO term request candidate. - subject_id: ARO:3000390 subject_label: rifampin ADP-ribosyltransferase (Arr) predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- GO's nearest term GO:0003950 is NAD+ poly-ADP-ribosyltransferase; Arr is a mono-ADP-ribosyltransferase acting on rifampin. No suitable mono term. GO term request candidate. - subject_id: ARO:3000445 subject_label: rifampin monooxygenase predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- GO has no rifampin/rifamycin monooxygenase MF term (only the general GO:0004497 monooxygenase activity). GO term request candidate. - subject_id: ARO:3000036 subject_label: tetracycline inactivation enzyme predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- GO has no Tet(X)/tetracycline-destructase (flavin-dependent tetracycline monooxygenase) MF term. GO term request candidate. - subject_id: ARO:3000202 subject_label: Cfr 23S ribosomal RNA methyltransferase predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- GO:0070040 is the C2 (RlmN housekeeping) 23S rRNA methyltransferase; Cfr methylates C8 of A2503. No C8-specific GO term. GO term request candidate. - subject_id: ARO:3002978 subject_label: D-Ala-D-Lac ligase predicate_id: skos:exactMatch object_id: sssom:NoTermFound object_source: obo:go.owl mapping_justification: semapv:ManualMappingCuration comment: >- VanA/B-type ligase makes D-Ala-D-Lactate; GO:0008716 is D-Ala-D-Ala ligase (wrong product). No D-alanine-D-lactate ligase GO term. GO term request candidate.