LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39431411", "kind": "science-record", "revision": 3, "content_hash": "sha256:763b6f991f235d4b19e7c9e8200051dc93a5b9c782134c3da3ee99ade8c854fe", "created_at": "2026-11-01T20:29:41Z", "updated_at": "2026-11-01T22:12:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins.", "doi": "10.1093/gbe/evae231", "pmid": "39431411", "authors": ["Łukasz F Sobala"], "journal": "Genome biology and evolution", "year": 2024, "abstract": "The origins and early evolution of animals are subjects with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from nonbilaterians. Publicly available data are plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic, and metagenomic studies and is an extension of EukProt (Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community J. 2022:2:e56. https://doi.org/10.24072/pcjournal.173). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections, whereas major updates will synchronize LukProt to each new version of EukProt, and releases are permanently stored on Zenodo (https://doi.org/10.5281/zenodo.7089120). A BLAST server to search the database is available at: https://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database aims to be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well.", "claims": [{"id": "claim-method", "statement": "Phylogenies were inferred using IQ-TREE 2.3.3.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39431411", "locator": "sections[15] \"Data Processing—20 BUSCOs Example\" paragraph 2", "quote": "Phylogenies were inferred using IQ-TREE 2.3.3."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data underlying this article (the LukProt database and supporting files) are available on Zenodo: https://doi.org/10.5281/zenodo.7089120 (Sobala 2022) and https://doi.org/10.5281/zenodo.11324807 (Sobala 2024).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39431411", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The data underlying this article (the LukProt database and supporting files) are available on Zenodo: https://doi.org/10.5281/zenodo.7089120 (Sobala 2022) and https://doi.org/10.5281/zenodo.11324807 (Sobala 2024)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "LukProt adopts the EukProt naming conventions and includes data from 216 additional animals.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39431411", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "LukProt adopts the EukProt naming conventions and includes data from 216 additional animals."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "LukProt adopts the EukProt naming conventions and includes data from 216 additional animals.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39431411"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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