This guide records the sources used for 74 database-derived annotation contexts. Manual decisions reside in FGA-ai-review.yaml; the source map retains source keys, indices and target routes without duplicating those decisions. Model coordinates refer to the represented entity, not an experimentally established processing schedule for every natural splice product.
| Source | Operative locator and access boundary |
|---|---|
| Reactome, 47 imported events | Each event's summation plus actual nested physical-entity definitions and compartments were read. The source map preserves the target-specific route. Unrelated branches were not exhausted, and not all literature cited by Reactome was independently read. |
| HPA, FGA/ENSG00000171560 | Subcellular record, Hep-G2, HPA051370 and HPA064755; both selected original immunofluorescence images viewed. ER assignment is supported; lumenal geometry and splice identity are unresolved. |
| InterPro IPR012290 and IPR037579 | Actual entry metadata, GO mappings and target P02671 match response. The coiled-coil match is residues 48–192; the family match spans 1–866. These are computational mappings, not additional experiments. |
| ARBA rules | Actual full condition alternatives and output terms were read for all 14 implicated rules. The matching FunFam branch is 4.10.530.10:FF:000002 with a human-compatible taxon. Canonical UniProt explicitly carries this match despite its gamma-chain label. Rule training publications were not reconstructed. |
| PAINT | Six exact IBD joins at PTN008715159 in PTHR47221. Official target membership and names are verified. Earlier target-to-node topology and MSA requests failed; newly recovered official sources now establish the PTN002499061-to-PTN008715159 path and exact 866-residue canonical sequence match. Prior failure receipts remain preserved. No donor-count or self-WITH argument is used. |
| UniProt | Preserved FGA record: subunit, secreted location, alternative products, signal/peptide/chain features, thrombin cleavage site and FunFam/InterPro cross-references. A gene-level annotation does not establish equivalent function of both natural splice products. |
| PMID:11601975 | Author-hosted original PDF: Methods, Results, Discussion and Figures 1–9 captions. Native chicken fibrinogen structure; alpha-C and mobile terminal regions unresolved. Normal cache remains abstract-only. No figure pixels or supplements independently read by this lane. |
| PMID:11170397 | Original identifier: genuine abstract and metadata only. Operative body remained inaccessible. The later paper's explicit preparation-dependent disagreement is recorded; original Methods are not claimed to have been read. |
| PMID:21806028 | Original full article: Experimental Procedures, oligomer characterization, tPA/plasminogen-binding Results and Figures 5–7, activation Results and Figure 8, relevant Discussion. Captions read here; ROOT separately viewed Figures 5–8 pixels. Bounded read, not every supplementary result. |
| PMID:37082262 | Original full article: Materials/Methods relevant to human proteins and assay context, truncated-chain characterization, Results 3.3/Figure 5 and relevant Discussion. ROOT separately viewed Figure 5 pixels. The entire set of other cellular and polymerization experiments was not independently assessed here. |
| PMID:19296670 | Original study: human-plasma source and crystallographic Methods; Results, Overall Structure. Proteolysis in crystals and unresolved alpha-C/terminal density are explicit. This lane did not inspect the full figure set or supplements. The complete manual reference is owned by the direct review. |
| PMID:6281794 | Original study: recovered original Results and Discussion, alpha-chain platelet interaction. Weaker alpha-chain activity and self-association limits are preserved; preparation details and complete reference assessment are owned by the direct review. |
| PMID:6777381 | Original author-hosted text: recovered Results, Figure 3 caption and Discussion comparing fibrinogen/fibrin with thrombospondin. Fibrinogen is explicitly converted to fibrin and detected on activated platelet surfaces. Complete Methods assessment belongs to the direct review. |
| PMID:10903502 | Original publisher text: adhesion/survival Methods, Table 1 and relevant Discussion in recovered indexed passages. Intact human fibrinogen, fragment D and gamma-chain peptide are distinguished. The indexed capture is discontinuous; it is not represented as a complete body read by this lane. |
| PMID:15739255 | Original publisher text: recovered Reagents and Antibodies, rat vessel Methods, Results/Figures 6–8 and Discussion. Human fibrinogen and fragment D are tested on rat vasculature. No alpha-chain-specific receptor-contact experiment is inferred. |
| PMID:19193866 | Preserved full normal: Reagents and Antibodies; endothelial culture, endothelin/vWF, WPB and ERK assay sections; Results associated with Figures 1–4. Human plasma fibrinogen was applied to rat heart microvascular endothelial cells. Figure pixels were not viewed by this lane. |
| PMID:8100742 | Positive original abstract only; operative original inaccessible. The existing contribution within the intact fibrinogen bridge is retained as non-core by explicit curator deference. Direct alpha-chain receptor contact and chain-resolved assay details remain uncertain; ancestry itself is not new biological evidence. |
The public ontology evidence contains actual official definitions and strict is_a/part_of paths used for broad-term decisions, plus the GO:0140767 enzyme-substrate adaptor child relationship to GO:0030674. The refinement uses independent human binding/coupled-activation evidence; it does not infer a new ancestral PAINT placement. The source snapshot records preserve dates and hashes. The general extracellular location remains useful across soluble fibrinogen, fibrin, released peptides and pathological variant-containing material. No single narrower complex term covers that entire source scope.
The curated fibrinopeptide A and mature-chain identifiers are separate from the two natural splice products. The product-source map preserves all six raw product-specific contexts and their exact seed joins. Experimental alpha-C fragments, cross-linked oligomers and proteolytic truncations remain experimental preparations.