Evidence claim

Site-Independent: description

Alignment-based model, fitted to a multiple sequence alignment of the protein family, that predicts mutation effects from each position separately, without the dependencies between positions that EVmutation adds.

Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

21 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Claimed field description Context-only references	Protocol metadata evidence: proteingym-paper.xml Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC10723403 retrieved 2026-09-23 Retrieved: 2026-09-23T18:43:10.260678+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `a58110e02c3efc8395c534d48630f577c3d45e90d48198b7f9989cf52600b045` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field description Context-only references	Abstract: Mutation effects predicted from sequence co-variation Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 Retrieved: 2026-10-11T00:38:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `6a91a29373ab03b0ebd3a03a7655536bd6abec369d1385146b4f94d1e0b5fbec` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. Inspected artifact
Claimed field description Context-only references	ProteinGym AMFR assay-level Spearman comparison Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-30	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `f432423b87f79ac9778dfac86e3d95be041d246bc618dc0a406b35b0b7466437` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Named prediction method identified in the cited primary source. Exact fitted configurations and scores are separate records. Context-only references	Protocol metadata evidence: proteingym-paper.xml Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC10723403 retrieved 2026-09-23 Retrieved: 2026-09-23T18:43:10.260678+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `a58110e02c3efc8395c534d48630f577c3d45e90d48198b7f9989cf52600b045` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Named prediction method identified in the cited primary source. Exact fitted configurations and scores are separate records. Context-only references	Abstract: Mutation effects predicted from sequence co-variation Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 Retrieved: 2026-10-11T00:38:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `6a91a29373ab03b0ebd3a03a7655536bd6abec369d1385146b4f94d1e0b5fbec` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. Inspected artifact
Previous value Named prediction method identified in the cited primary source. Exact fitted configurations and scores are separate records. Context-only references	ProteinGym AMFR assay-level Spearman comparison Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-30	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `f432423b87f79ac9778dfac86e3d95be041d246bc618dc0a406b35b0b7466437` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Context-only references	Protocol metadata evidence: proteingym-paper.xml Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC10723403 retrieved 2026-09-23 Retrieved: 2026-09-23T18:43:10.260678+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `a58110e02c3efc8395c534d48630f577c3d45e90d48198b7f9989cf52600b045` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Context-only references	Abstract: Mutation effects predicted from sequence co-variation Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017 Retrieved: 2026-10-11T00:38:38Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `6a91a29373ab03b0ebd3a03a7655536bd6abec369d1385146b4f94d1e0b5fbec` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. Inspected artifact
Source location profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Context-only references	ProteinGym AMFR assay-level Spearman comparison Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-30	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `f432423b87f79ac9778dfac86e3d95be041d246bc618dc0a406b35b0b7466437` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value Alignment-based model, fitted to a multiple sequence alignment of the protein family, that predicts mutation effects from each position separately, without the dependencies between positions that EVmutation adds. Context-only references	Protocol metadata evidence: proteingym-paper.xml Original source ↗ profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC10723403 retrieved 2026-09-23 Retrieved: 2026-09-23T18:43:10.260678+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `a58110e02c3efc8395c534d48630f577c3d45e90d48198b7f9989cf52600b045` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

3 source records and release history

ProteinGym AMFR assay-level Spearman comparison · Original source · 144fe22b07dfaeec2b366f2346203a9838a55b4c
Abstract: Mutation effects predicted from sequence co-variation · Original source · Europe PMC core record MED/28092658 (title and abstract), Nature biotechnology 2017
Protocol metadata evidence: proteingym-paper.xml · Original source · PMC10723403 retrieved 2026-09-23

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Technical metadata and extraction receipts

Stable ID: metadata-correction-fbaafadc4cef4f56932a

areas: proteins-complexes
field: description
previous value: Named prediction method identified in the cited primary source. Exact fitted configurations and scores are separate records.
value: Alignment-based model, fitted to a multiple sequence alignment of the protein family, that predicts mutation effects from each position separately, without the dependencies between positions that EVmutation adds.
source locator: profile-protocol-proteingym-paper-xml-a58110e0: Baselines ('Alignment-based models, such as site-independent and EVmutation models [Hopf et al., 2017] ... are trained on Multiple Sequence Alignments'); qa-descriptions-20261011-a-source-hopf2017: abstractText (EVmutation 'explicitly captures residue dependencies between positions'; most methods 'do not consider the interdependencies of residues')
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude integrator agent for issue #88. Reviewer: a separate Claude review agent, independent of the extractor; no human review claimed.; date: 2026-10-11; method note: Compared the store diff with origin/main, read each new description against its cited source passage and checked the licence of each new source record.; note: Approved. Checked the 10 method and model descriptions against their sources (EVmutation, GEMME and RSALOR abstracts, the FramePool k-mer random forests, the RhoMax BLASSO text) and spot-checked the 49 mRNABench rows against Appendix A; all accurate. Licences on the 3 new sources match their Europe PMC records. At the reviewer's suggestion, the en dash printed in some checkpoint names is written as a hyphen in the descriptions.; receipt: data/omics/qa-descriptions-20261011-a/review.json

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subject: Site-Independent

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