gene wiki and wikimedia foundation sparql workshop
TRANSCRIPT
![Page 1: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/1.jpg)
CURATING BIOMEDICAL KNOWLEDGE ON WIKIDATA AND WIKIPEDIA
GENE WIKI
Benjamin GoodThe Scripps Research Institute, La Jolla, California
[email protected]: @bgood
![Page 2: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/2.jpg)
Gene Wikidata TeamAndrew Su (Scripps)
Andra Waagmeester (Micelio)Sebastian Burgstaller (Scripps)Tim Putman (Scripps) – speaking next Julia Turner (Scripps)
Elvira Mitraka (U Maryland)Justin Leong (UBC)Lynn Schriml (U Maryland)Paul Pavlidis (UBC)Ginger Tsueng (Scripps)
ACKNOWLEDGEMENTS
![Page 3: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/3.jpg)
“knowledge”
• A lot
• Important
• Text
![Page 4: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/4.jpg)
More than 2 articles published/minute
![Page 5: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/5.jpg)
Documents
Concepts
Gene Wiki: Filtering and summarizing PubMed
![Page 6: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/6.jpg)
GENE WIKI
6
Protein structure
Symbols and identifiers
Tissue expression pattern
Gene Ontology annotations
Links to structured databases
Gene summary
Protein interactions
Linked references
Huss, PLoS Biol, 2008
Bot!
![Page 7: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/7.jpg)
GENE WIKI TIMELINE
2007
Project Starts
2008
ProteinBoxBot populates infoboxes
for 9,000 human genes
Now at 10,369 genes, analyses
show article growth and high quality
20112009
Updated Bot maintaining
9,678 human genes
Start importing gene data into wikidata
20142016a
Convert more than 11,000+ gene infoboxes on
Wikipedia to draw all content from Wikidata
2016b
Launch first biomedically focused
Web App driven by Wikidata content…
https://en.wikipedia.org/wiki/Portal:Gene_Wiki
![Page 8: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/8.jpg)
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 11,000+ genes
=
(1 of these for every gene)
IMPACT OF WIKIDATA ON WIKIPEDIA
![Page 9: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/9.jpg)
IMPACT BEYOND WIKIPEDIA= SPARQL
![Page 10: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/10.jpg)
Sample of current biomedical content
• All human, mouse genes and proteins• All Gene Ontology terms (describe function)• All Human Disease Ontology terms• All FDA approved drugs • 109+ reference microbial genomes
Burgstaller-Muelbacher et al (2016) DatabaseMitraka et al (2015) Semantic Web Applications for the Life Sciences
Putman et al (2016) Database
![Page 11: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/11.jpg)
http://tinyurl.com/biowiki-sparql
Sample queries that are currently possible:• “where in the cell is the Reelin protein expressed?”• “What diseases are treated by Metformin”• “What diseases might be treated by Metformin”
http://query.wikidata.org
![Page 12: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/12.jpg)
Example question: repurposing Metformin
http://tinyurl.com/zem3oxz
Metformin
?disease
interacts with
protein
geneencoded by genetic association
Mighttreat ?
Solute carrier family 22
member 3
SLC22A3
prostate cancer
![Page 13: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/13.jpg)
![Page 14: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/14.jpg)
A SPARQL powered user interface for consuming and editing organism data in WikidataTimothy E. Putman Ph.D. The Scripps Research Institute, La Jolla, California
[email protected]: @putmantime
![Page 15: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/15.jpg)
Gene Wikidata TeamAndrew Su (Scripps)Benjamin Good – just spokeAndra Waagmeester (Micelio)Sebastian Burgstaller (Scripps)Elvira Mitraka (U Maryland)Julia Turner (Scripps)Justin Leong (UBC)Lynn Schriml (U Maryland)Paul Pavlidis (UBC)Ginger Tsueng (Scripps)
ACKNOWLEDGEMENTS
![Page 16: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/16.jpg)
Centralizing and Linking the Data
BacteriaQ10876domain
TRPAQ21153984protein
C.trachomatisQ131065species
trpAQ21153861gene
C. trachomatis434/BUQ20800254strain
![Page 17: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/17.jpg)
C. trachomatisQ131065species
trpAQ21153861gene
TRPAQ21153984protein
C. trachomatis434/BUQ20800254strain
![Page 18: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/18.jpg)
trpAQ21153861gene
TRPAQ21153984protein
C. trachomatis434/BUQ20800254strain
C. trachomatisQ131065species
![Page 19: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/19.jpg)
C. trachomatisQ131065species
TRPAQ21153984protein
C. trachomatis434/BUQ20800254strain
trpAQ21153861gene
![Page 20: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/20.jpg)
C. trachomatisQ131065species
trpAQ21153861gene
C. trachomatis434/BUQ20800254strain
TRPAQ21153984protein
![Page 21: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/21.jpg)
![Page 22: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/22.jpg)
SPARQL Query• On page load
• JQuery execution of SPARQL query as AJAX GET Request
![Page 23: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/23.jpg)
![Page 24: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/24.jpg)
• On organism select• Get all gene and protein data for organism by
taxid
![Page 25: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/25.jpg)
![Page 26: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/26.jpg)
![Page 27: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/27.jpg)
![Page 28: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/28.jpg)
![Page 29: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/29.jpg)
![Page 30: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/30.jpg)
![Page 31: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/31.jpg)
![Page 32: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/32.jpg)
![Page 33: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/33.jpg)
![Page 34: Gene Wiki and Wikimedia Foundation SPARQL workshop](https://reader036.vdocuments.site/reader036/viewer/2022062522/587b37de1a28ab057d8b769d/html5/thumbnails/34.jpg)
QUESTIONS?