SCIdude

"things, not strings"

Amit Singhal

Hello, I'm trying to improve the molbio part of Wikidata by manual and batch editing. Although being a software dev (main language C++), I have prepared many books for Project Gutenberg (Q22673), contributed in the years 2006-2012 to German Wikipedia (Q48183) (as User:Ayacop), and also have biocurated extensively for UniProt-GOA (Q28018111) and Reactome (Q2134522).

Ralf Stephan (Q67363620)

Babel user information
de-N Dieser Benutzer spricht Deutsch als Muttersprache. en-3 This user has advanced knowledge of English. fr-1 Cet utilisateur dispose de connaissances de base en français. la-1 Hic usor simplici lingua Latina conferre potest. ru-0 Этот участник не владеет русским языком (или понимает его с трудом). it-0 Questo utente non è in grado di comunicare in italiano (o lo capisce solo con notevole difficoltà). This user is a member of WikiProject Microbiology. This user is a member of WikiProject Molecular biology. This user is a member of WikiProject Chemistry. This user is a member of WikiProject COVID19.
Users by language

• Wikidata:WikiProject_COVID-19/Items
• Wikidata:WikiProject_Schemas
• Wikidata:WikiProject_Chemistry/Natural_products
• Wikidata:Database_reports/Complex_constraint_violations/P235#Modified_unique_value_constraint
• petscan Proteins(EN)

Current ideas:

• User:SCIdude/Imports
• User:SCIdude/Protein bugs
• User:SCIdude/Modeling
• User:SCIdude/Maintaining
• User:SCIdude/WP-Orphans
• User:SCIdude/ChEBI-conflicts
• User:Scidudebot

• check WP links in GO
• for every GO complex, list parts and make subunit families
  • eyeball GO components with 'complex', equal to subc-of-complex?
• pfam with func carbohydrate bindng physically interacts with carbohydrate (GO: intersection_of: GO:0005488 ! binding|intersection_of: has_input CHEBI:16646 ! carbohydrate
• instance of protein fragment with 'of"
• construct accessible pipe for verifying TCDB ID of proteins / families
• complexes from PRotein Ontology
• MeSH protein entries are usually species-independent. Check heuristically and use
• connect Reactome entities with existing families
• Arabidopsis and Dictyostelium import
• incomplete ChEBI: add reference for all InChi leys, InChi, isomeric SMILES, can.SMILES
• incomplete ChEBI: add reference for all (subst is-a class)
• incomplete ChEBI: add reference for all (class subc-of class)
• ChEBI: import completion, full class hierarchy
• ChEBI: import completion, all substances
• ChEBI: check all substances are in their classes
• PMCREF: use https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2685584
• use "substrate of"
• subc-of-enzyme inhibitor + phys. interact. with XY --> inhibitor of XY
• subc-of-agonist + phys. interact. with XY --> agonist of XY
• use subc to describe pgroups exactly
• UniProt protein families
• sync prot-->part of-->enzfam if exact molfunc is annotated
• multifunctionnal enzymes?
• some proteins encoded by same gene, mark as variants
• interpro and superfamily with description "InterPro Domain"---> really are domain superfamilies
• check IPR items for correct Pfam (via IPR), also move Pfam from other item
• GO items with changed label are suspected to be WPedians fumbling result
• if TCDB fam X subclass-of TCDB fam Y --> missing reference dbhierarchy heuristics
• Reactome candidate sets missing "has part"
• peptidases with endopep func
• IUPHAR IDs without Wikidata, anyone?
• IUPHAR family IDs, anyone?
• mebranome classes https://membranome.org/
• add "stated as" qual. to ChEBI ids of amino acids / their zwitterions; make special contraint including this
• BindingDB ids?
• dbSNP import?
• missing OMIM phenotypes, e.g. 1?
• OMIM phenotypic series, see their FAQ
• orthology group ids/groups, see bot issue
• do all ions have charge in their label?
• next MONDO sync?
• german labels from Brockhaus
• remove em-dashes from labels
• items with dewiki but without enwiki and en-label
• industry processes don't have-parts all reactants/modifiers

In the manual attempt to create/curate WD items of cleavage products (fragments) of proteins I worked around insulin (Q7240673), Angiotensinogen (Q267200), Ghrelin and obestatin prepropeptide (Q66216544), proglucagon (Q66310097), Proopiomelanocortin (Q418896), Cerebellin 1 precursor (Q21115606), Natriuretic peptide B (Q422288), Endothelin 1 (Q66361339), Apelin (Q2386988), Tachykinin precursor 1 (Q21123080), Secretogranin II (Q21105303), Thymosin beta 4 X-linked (Q7799643), Vasoactive intestinal peptide (Q66499176), VGF nerve growth factor inducible (Q21122290), augurin precursor (Q66535298), Chromogranin A (Q3698322), Cathelicidin antimicrobial peptide (Q411181)

What I'm doing is roughly this:

• if gene and protein is in one item, duplicate to get separate items (moving sitelinks first to the protein)
• remove wrong statements on either (e.g. no PDB/protein IDs/GOA function/localization annotations on genes), make sure the gene has at the most GO process annotations
• create/check all relevant fragment objects, move statements to the resp. item: EnsemblP should be on prepro/pro
• separate out aliases to resp. objects
• add "has part" with all fragments to prepro object
• complete "encodes/encoded by" everywhere
• add "exact match" qualifier to fragment UniProt like e.g. https://www.uniprot.org/uniprot/Q9UBU3#PRO_0000019202
• add Reactome, ChEBI, ChemBL, IUPHAR IDs to fragment if existing (Reactome labels like GENE(1-100) also to fragment aliases)
• add "part of" Reactome process or reaction if missing
• (maybe) move GOA function annotations to resp. fragment if applicable

misc

{{section resolved|~~~~}} {{Q|21105303}}

• https://www.mediawiki.org/wiki/Wikibase/Indexing/RDF_Dump_Format#Data_model