# Curated analysis-type calls for references behind RCA annotations in GOA. # Read by rca_source_catalog.py; a call here overrides the title keyword rules. # Covers every reference with >=5 RCA rows (QuickGO download of 2026-10-05), each judged # from its PubMed abstract (and, for proteomics papers, from what GOA asserts from it). # # Classes: # proteomics MS identification/quantification of a fraction, tissue or organelle [omics] # interactomics co-complex / affinity-purification / co-fractionation MS [omics] # transcriptomics expression profiling [omics] # genetic_screen genome-scale mutant/phenotype screens [omics] # other_omics other high-throughput experimental data (e.g. fusion-reporter screens) [omics] # proteome_scale_prediction genome/proteome-wide *computational* prediction (classifier, motif, # domain scan); any experiment in the paper is validation of a subset # family_or_genome_survey sequence analysis of one gene family or one genome's repertoire # pathway_or_metabolic_model pathway database / metabolic reconstruction # single_gene_study cloning/characterisation of one gene, operon or a few paralogs # unresolved could not determine what the reference is GO_REF:0000123: class: pathway_or_metabolic_model title: YeastPathways to GO-CAM conversion note: >- SGD pathway GO-CAMs exported to GAF; WITH/FROM = SGD_PWY:*. A curated pathway model is not a computational analysis of large-scale data; IC or TAS-like pathway evidence would describe it better than RCA. Treated as a quirk, not studied here. PMID:20660476: class: proteome_scale_prediction note: >- SVM classifier for mitochondrial localization (T. brucei MitoCarta); RNA-seq in the same paper measures expression, not location. All 1,039 rows are CC mitochondrion. PMID:30358795: class: proteome_scale_prediction note: >- Zinc proteome "identified using a bioinformatics analysis that combined global domain searches with local motif searches"; mass spectrometry in the same paper measured abundance only. The GO term (zinc ion binding) comes from the prediction. PMID:21166475: class: proteomics note: >- LC-MS/MS of the Arabidopsis cytosolic fraction. All 436 GOA rows are NOT|located_in cytosol, i.e. assertions about proteins *outside* the robust set. PMID:11738814: class: proteome_scale_prediction note: PATS apicoplast-targeting predictor (neural network on sequence features). PMID:22430844: class: proteomics note: >- Arabidopsis Golgi proteomics; the paper reports ~19% of identified proteins as likely contaminants. All 191 GOA rows are NOT|located_in Golgi apparatus. PMID:25037231: class: proteomics note: ECM-enrichment proteomics of colon cancer and liver metastases (BHF-UCL matrisome set). PMID:27510400: class: proteome_scale_prediction note: >- Membranome database of computationally modelled single-pass TM proteins; title rule mis-calls it proteomics. 119 rows of CC plasma membrane (E. coli). PMID:22159717: class: proteomics note: >- Matrisome paper: proteomics of murine ECM *and* the in-silico matrisome definition whose categories the BHF-UCL term mapping follows (see rca_matrisome_crosswalk.py). PMID:28071719: class: proteomics note: Quantitative ECM proteomics of pancreatic islets (mouse). GO_REF:0000028: class: unresolved note: PAMGO_MGG (Magnaporthe) GO_REF; title not resolved; mostly broad BP terms. PMID:28675934: class: proteomics note: ECM proteomics protocol paper (normal and diseased human tissues). PMID:21761556: class: proteomics note: >- Bombyx mori integument/trachea/scale LC-MS/MS; FlyBase-assigned rows on silkworm proteins assert structural constituent of chitin-based cuticle plus the cuticle CC. PMID:26991453: class: interactomics note: Co-fractionation MS protein complex map of T. brucei; rows assert mitochondrial mRNA editing complex. PMID:19834910: class: proteomics note: LC-MS/MS of T. brucei mitochondrial membrane fractions; subset validated by tagging. PMID:20551380: class: proteomics note: Human aorta ECM proteomics. PMID:12819136: class: family_or_genome_survey note: Mouse/human domain-family comparison of apoptosis genes (orthology inference). PMID:27559042: class: proteomics note: Glycoproteomics of human atrial ECM. PMID:28327460: class: proteomics note: Proteomics of stem-cell-derived ECM. PMID:15718104: class: family_or_genome_survey note: TAAR receptor family phylogeny across species. PMID:17107762: class: single_gene_study note: Nine cotton EF1A cDNAs, sequence + qRT-PCR. PMID:17919451: class: family_or_genome_survey note: Bioinformatic inventory of P. falciparum translocation machinery (review). PMID:27068509: class: proteomics note: Varicose vein ECM proteomics. PMID:22261194: class: proteomics note: Porcine cardiac ECM proteomics. PMID:30715439: class: single_gene_study note: SCOOP12 peptide family; in-silico family identification plus one characterised member. PMID:21725637: class: single_gene_study note: Cotton profilin genes. PMID:17363967: class: single_gene_study note: T. brucei elongase fatty-acid synthesis (review of a pathway). PMID:23979707: class: proteomics note: SILAC proteomics of endothelial cell morphogenesis incl. secreted ECM. PMID:18364711: class: pathway_or_metabolic_model note: Leishmania major metabolic network reconstruction. PMID:19103232: class: family_or_genome_survey note: P. falciparum Qa-SNARE family; locations predicted from alignments, one verified. PMID:9593292: class: family_or_genome_survey note: E. coli ABC protein repertoire from the genome sequence. PMID:15919996: class: other_omics note: >- E. coli inner-membrane proteome topology from PhoA/GFP C-terminal fusions of 601 proteins (large-scale experimental reporter screen) constraining a predictor. PMID:29514851: class: single_gene_study note: PdeC / CSS-domain phosphodiesterases. DOI:10.1016/j.mbplus.2018.11.001: class: proteome_scale_prediction title: The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification note: In-silico C. elegans matrisome (title via Crossref); WB rows include ECM structural constituent. PMID:19585695: class: family_or_genome_survey note: Aspergillus nidulans cell-wall gene inventory. PMID:7536291: class: single_gene_study note: dpp operon sequence and expression. PMID:15064375: class: single_gene_study note: Maize cytokinin receptor histidine kinases. PMID:21136929: class: proteomics note: P. falciparum food vacuole proteome. PMID:17005920: class: single_gene_study note: Maize 13-lipoxygenases. PMID:21029107: class: single_gene_study note: Cotton blue copper-binding proteins. PMID:17943315: class: single_gene_study note: Cotton MADS-box transcripts. PMID:9387241: class: single_gene_study note: E. coli hyf operon sequence. PMID:14702297: class: single_gene_study note: E. coli BetU and osmoregulatory transporters. PMID:12649499: class: interactomics note: Purification and MS identification of T. brucei editosome components. PMID:9529885: class: family_or_genome_survey note: Major facilitator superfamily phylogeny. PMID:2092358: class: single_gene_study note: E. coli cellobiose permease operon. PMID:16603573: class: proteomics note: Metabolic-labelling proteomics plus prediction of GPI-anchored P. falciparum proteins. PMID:19288220: class: single_gene_study note: Cotton cdh-like gene. PMID:9620272: class: single_gene_study note: Maize LON1 protease. PMID:11244102: class: family_or_genome_survey note: Maize aquaporin family. PMID:19497128: class: pathway_or_metabolic_model note: LeishCyc pathway database. PMID:17927906: class: single_gene_study note: Cotton kinesin GhKCH2. PMID:19294420: class: family_or_genome_survey note: Plasmodium ER-retrieval signal families predicted from sequence; GFP proof of principle. PMID:19578975: class: single_gene_study note: Cotton PPR genes. PMID:8057835: class: single_gene_study note: nrf operon. PMID:2188958: class: single_gene_study note: cysTWAM sulfate transport genes. PMID:1838574: class: single_gene_study note: fep ferric enterobactin transport genes. PMID:33543001: class: proteome_scale_prediction note: Same in-silico C. elegans matrisome paper as the DOI entry, cited by PMID. PMID:16573693: class: single_gene_study note: Two PHB-domain complexes of the E. coli membrane (title rule mis-calls interactomics). PMID:23202856: class: single_gene_study note: c-di-GMP-stimulated interaction in exopolysaccharide synthesis (title rule mis-calls interactomics).