Wikidata workshop for ISB Biocuration 2016
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This document discusses using Wikidata as a platform for biocuration. Wikidata is presented as a new paradigm that could reduce pain points in current biocuration practices by providing a single platform with persistent data access. It describes Wikidata's structure as a knowledge base of unique items and statements linked together to form a knowledge graph. Examples show how biomedical data like genes and proteins are represented. The document outlines Wikidata's community processes and increasing impact on applications like Wikipedia and genome browsers. It envisions the potential for researchers to contribute new biomedical knowledge through Wikidata.
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Wikidata workshop for ISB Biocuration 2016
- 1. Wikidata as a platform for biocuration Benjamin Good The Scripps Research Institute @bgood
- 2. Organization , more information http://tinyurl.com/biocuration-wikidata • Part 1: getting to know wikidata • A platform for biocuration (Ben Good) • Wikipedia and Wikidata for research (Daniel Mietchen) • Editing Wikidata (Sebastian Burgstaller-Muelbacher) • Coffee Break • Part 2: getting your hands on wikidata: flash biocuration jamboree!
- 3. API Flatfiles The dominant paradigm for open biocuration API Flatfiles Your Database Your Database Your Databasexrefs Your Database Pain points • API or flatfile parsing • Ambiguous or non-existent xrefs • Persistence of funding • Too much information to curate My Web Application My Database My Database Curators My Research Grants $ Biomedical knowledge
- 4. A new paradigm for open biocuration? Our Applications Our Database? Our Database Curators And our community Biomedical knowledge Our Applications Our Applications My Research Grants $ Reducing the pain • Reduces API/parser proliferation • Forces up-front integration • Facilitates coordination • Ensures that if funding is lost, data is not • Invites community input
- 5. A new platform for open biocuration? Our Applications Our Database Curators And our community Biomedical knowledge Our Applications Our Applications My Research Grants $
- 6. Is to data as Wikipedia is to text “Giving more people more access to more knowledge” A free and open repository of knowledge • Initiated by WikiMedia Germany • In transition to the WikiMedia Foundation • Not a ‘project’… as stable as Wikipedia
- 7. It’s a knowledge base! • Anyone can edit (human or robot) • Anyone can use (CC0)
- 8. Elements of the kb are called ‘items’ • Labels and descriptions in many languages
- 9. Items are unique concepts, used to link different language Wikipedias together Q146 Af:Kat En:cat Als:Hauskatze Ang:Catte Av:Keto
- 10. Items are described by “statements” that link together to form the language-independent wikidata knowledge graph Cat Domesticated Animal Animal Subclass Of Subclass Of Animalia Taxon name Kingdom Taxon rank
- 11. Item: Q84
- 12. Item: Q414043 RELN Genomic start: 103471784 GenLoc assembly: GRCh38 Stated in: Ensembl Release 83 Retrieved: 19 January 2016 Value (numeric) Property Claim Qualifiers References https://www.wikidata.org/wiki/Q414043 Statement Genomic position for Reelin gene
- 13. Item: Q414043 RELN Encodes: Reelin (protein) Stated in: NCBI homo sapiens annotation release 107 Retrieved: 19 January 2016 Value (item) Property Claim Qualifiers References https://www.wikidata.org/wiki/Q414043 Statement Linking the Reelin gene to a protein it encodes
- 14. Item: Q13561329 Reelin Cell component: dendrite Determination method: • ISS (Sequence or structural Similarity) • IEA (Electronic annotation) Stated in: Uniprot Retrieved: 21 March 2016 Value (item) Property Claim Qualifiers References https://www.wikidata.org/wiki/Q13561329 Statement Gene ontology annotation for Reelin protein with evidence codes modeled as qualifiers
- 15. graphical view RELN Reelin encodes dendrite cellular component claim ISS IEA Determination method: qualifiers UniProt stated in retrieved 21 March 2016 References Statement
- 16. Questions about wikidata structure?
- 17. Inter-item links form a giant knowledge graph Everything is connected Reelin, Heart disease, Barack Obama, everything.. https://query.wikidata.org SPARQL endpoint for Wikidata
- 18. “GO cellular localization annotations for Reelin with evidence code ISS” from http://query.wikidata.org http://tinyurl.com/biowiki-sparql
- 19. ISS GO cellular localization annotations for Reelin
- 20. RELN Reelin encodes dendrite cellular component claim ISS IEA Determination method: qualifiers UniProt stated in retrieved 21 March 2016 References Statement SPARQL graph.. http://tinyurl.com/biowiki-sparql
- 21. “GWAS-based disease associations for Reelin” http://tinyurl.com/biowiki-sparql
- 22. “GWAS-based disease associations for Reelin”
- 23. A new platform for open biocuration? Our Applications Our Database Curators And our community Biomedical knowledge Our Applications Our Applications My Research Grants $ • SPARQL = a common API for accessing content • 1 endpoint to maintain… • Its working
- 24. Wikidata and the Semantic Web • Hub for linked open data • A lot of initial contents are identifier links (e.g. we link drug items to 18 different schemes) • e.g. see Vemurafenib • Supports federated queries – e.g. you can do one query that spans wikidata content and uniprot RDF content On its way to replacing Dbpedia as the central node
- 25. Questions about wikidata and the semantic web ?
- 26. Social controls • Anyone can • Add or edit labels, descriptions, statements, references etc. on existing items • Create new items • Link items to Wikipedia articles • Query using https://query.wikidata.org • Read and write small numbers of edits with https://www.wikidata.org/w/api.php • Propose a new property • Request a bot account for high-volume automated editing Here be dragons..
- 27. Properties (as of April 10, 2016) • 2196 active properties • 114 new properties that have been proposed but not yet approved Proposal https://www.wikidata.org/wiki/Wikidata:Property_proposal
- 28. After proposal, community discussion • Each property is left open for discussion by anyone until • An administrator or other person blessed with the power either creates it or decides not to create it based on the discussion • People that enjoy ontology arguments needed here! Lengthy (cut-off) discussion of proposal for ‘extinct’ property
- 29. https://www.wikidata.org/wiki/Wikidata:Property_proposal/ Property proposal on wikidata Proposal Community discussion
- 30. Bot accounts • https://www.wikidata.org/wiki/Wikidata:Requests_for_permissions/Bot • Same basic process.
- 31. Proposal discussions • Can not be avoided • The discussions are long and tiring but important • Many of the people involved are quite experienced • All are trying to make something great • Persistence and patience required
- 32. Questions on community processes? • (more to come)
- 33. The first application built on wikidata, Wikipeda Our Database Curators And our community Biomedical knowledge Our Applications Our Applications Su, Schriml, Pavlidis R01 Grant… $
- 35. Application #1 Burgstaller et al (2016)
- 36. Impact of wikidata on Wikipedia Gene Wiki Version 1. {{GNF_Protein_box | Name = Reelin| image = | image_source = | PDB = {{PDB2|4AD9}} | HGNCid = 18512 | MGIid = | Symbol = LACTB2 | AltSymbols =; CGI-83 | IUPHAR = | ChEMBL = | OMIM = None | ECnumber = | Homologene = 9349 | GeneAtlas_image1 = | GeneAtlas_image2 = | GeneAtlas_image3 = | Protein_domain_image = | Function = {{GNF_GO|id=GO:0005515 |text = protein binding}} {{GNF_GO|id=GO:0016787 |text = hydrolase activity}} {{GNF_GO|id=GO:0046872 |text = metal ion binding}} | Component = {{GNF_GO|id=GO:0005739 |text = mitochondrion}} | Process = {{GNF_GO|id=GO:0008152 |text = metabolic process}} | Hs_EntrezGene = 51110 | Hs_Ensembl = ENSG00000147592 | Hs_RefseqmRNA = NM_016027 | Hs_RefseqProtein = NP_057111 | Hs_GenLoc_db = hg38 | Hs_GenLoc_chr = 8 | Hs_GenLoc_start = 70635318 | Hs_GenLoc_end = 70669174 | Hs_Uniprot = Q53H82 | Mm_EntrezGene = 212442 | Mm_Ensembl = ENSMUSG00000025937 | Mm_RefseqmRNA = NM_145381 | Mm_RefseqProtein = NP_663356 | Mm_GenLoc_db = mm10 | Mm_GenLoc_chr = 1 | Mm_GenLoc_start = 13623330 | Mm_GenLoc_end = 13660546 | Mm_Uniprot = Q99KR3 | path = PBB/51110}} = Gene Wiki Version 2. {{Infobox gene}} • All data in Wikidata • 1 Lua script works for all genes = (1 of these for every gene)
- 37. Wikidata use increasing on Wikipedia • https://en.wikipedia.org/wiki/Category: Templates_using_data_from_Wikidata • 81 templates indicate that they use it
- 38. Questions about Wikidata and Wikipedia?
- 39. Application #2 Web Apollo Genome Browser 39Putman et al (2016)
- 40. The next application built on wikidata, yours? Our Database Curators And our community Biomedical knowledge ???? ???? $ My Research Grants Its your data as much as anyone else’s!
- 41. Current state: seeding nodes for the graph • All human, mouse genes and proteins (swissprot) • All Gene Ontology terms • All FDA approved drugs • All Human Disease Ontology terms • 109 reference microbial genomes Burgstaller-Muelbacher et al (2016) Database Mitraka et al (2015) Semantic Web Applications for the Life Sciences Putman et al (2016) Database
- 42. Next data step: connecting the nodes • Our group • Human: Gene-disease (PhenoCARTA team) • Human: Drug-disease (CHEMBL, NDF-RT) • Human: Gene-drug (CHEMBL, NDF-RT) • Expanding microbial information (Putman, Koehurst, Knight lab) • Your group • ? • Today • A knowledge base for understanding Zika ?
- 43. Acknowledgements Gene Wikidata Team Andra Waagmeester (Micelio) * Sebastian Burgstaller (Scripps) * Tim Putman (Scripps) * Elvira Mitraka (U Maryland) Julia Turner (Scripps) Justin Leong (UBC) Lynn Schriml (U Maryland) Paul Pavlidis (UBC) Andrew Su (Scripps) Ginger Tsueng (Scripps) Contact bgood@scripps.edu @bgood on twitter* First author on manuscript cited in this presentation Adapted logo Su Laboratory at TSRI The 16,950 other active editors of Wikidata and especially the 693 that joined last month and the 809 that joined the month before that and the 721 that joined the month before that..
Notas del editor
- Wikidata: Advancing science through semantic integration of genes, diseases, and drugs
- This is the central point I want to make. Wikidata can be used to to build knowledge-based applications, lowering the barrier to entry for building apps and reducing challenges of downstream data integration. Before coming back to this, I will explain why.
- This is the central point I want to make. Wikidata can be used to to build knowledge-based applications, lowering the barrier to entry for building apps and reducing challenges of downstream data integration. May
- This is the central point I want to make. Wikidata can be used to to build knowledge-based applications, lowering the barrier to entry for building apps and reducing challenges of downstream data integration. Before coming back to this, I will explain why.
- By mixing the data into wikidata, we reduce API proliferation, easing application formation. Over 1 billion triples Fast Stable since around September 2015
- Successor to DBpedia Simplest and first use case are identifier mapping Supports linking of distributed linked data sets
- By mixing the data into wikidata, we reduce API proliferation, easing application formation. Over 1 billion triples Fast Stable since around September 2015
- This is the first application of the work that we have done
- By mixing the data into wikidata, we reduce API proliferation, easing application formation. Over 1 billion triples Fast Stable since around September 2015