The Stone Soups of Programmers (hackathons) and Data (WikiData). Presented at Heart BD2K PI meeting, EBI, Feb. 22, 2016

1. Channeling
Collaborative Spirit
Benjamin Good
The Scripps Research Institute

2. Menu
• The Stone Soup of Programmers
• The Stone Soup of Data
Stone Soup
Credit: Jamie Taylor of MetaWeb, WWW2007, The Stone Soup of Data

3. Hackathons
http://baltimorehackathon.com/

4. Mashups, Collaborations
PSEA-Quant
MyGene.info
XI
PSICQUIC
PINT
IBminer
EGA
Train Online
?
?
?
?
?
?

5. Recent BD2K sponsored hackathons
• Palo Alto, November 2015, Network of BioThings 4
• La Jolla, January 2016, Web Apollo
• Boston, February 2016, Morphological profiling data analysis
• Buenos Aires, April 2016, UCLA Heart Bits
• Cambridge, MA, April 2016, Hacking Cancer: TCGA and 7 Bridges

6. Winner!
Palo Alto, November 2015,
(Network of BioThings 4)
https://github.com/Networkof
BioThings/conceptcentricview
http://ccv.bioontology.org/
Concept Centric View
“CCV”
Search for “heart”

7. La Jolla, January 2016, Web Apollo
No judging this time, just my favorite..
Genome Annotations grabbed from remote SPARQL endpoint, rendered in Web Apollo

8. Hackathon status: going well

9. Please keep in mind
For
• Networking
• Rapid prototyping
• Scheming and talking
Not for
• Good software
engineering…
• Makes a bit of a mess..

10. Menu
• The Stone Soup of Programmers
• The Stone Soup of Data

11. Stone Soup(s) of Data: ingredients
• A lot to choose
from! (NAR lists
1,500+)
• Can be tasty!
Disease …. Target gene

12. Hard to mix…
Your new database here..

13. Some ingredients get lo$t..
Your new database here..

14. My Soup!

15. To build Data Soups
• We need to integrate data from different sources
• We need the data to remain accessible
• We need people to:
• eat our soup (use our data..)
• pay for it
• help us improve our recipe

16. Knowledge Commons
A common place for:
• Storing identifier mappings
• Hosting knowledge for the long term
• Channeling collaborative spirit !

17. Knowledge Commons

18. Is to data
as Wikipedia is to text
“Giving more people more access to more knowledge”
A free and open repository of knowledge
Managed by the MediaWiki foundation
that operates Wikipedia
Not a ‘project’…

19. It’s a knowledge
base!
• Anyone can edit
(human or bot)
• Anyone can use
(CC0)

20. Item: Q84

21. 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

22. 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

23. Inter-concept links form a knowledge graph

24. Adding data manually
(1) Find a concept,
(2) edit

25. Once the data is in, it joins a GGG
https://query.wikidata.org = SPARQL endpoint for Wikidata
Giant
Global
Graph
Everything is
connected,
Reelin, Heart
disease,
Barack Obama,
everything..

26. We are seeding it with
biomedical data
• All human, mouse genes and proteins
• All Gene Ontology terms
• All FDA approved drugs
• 9,000+ human diseases
• 120 reference microbial genomes
Burgstaller et al (2016) Database (preprint in BioRxiv)
Mitraka et al (2015) Semantic Web Applications for the Life Sciences (best paper) (preprint in BioRxiv)
Putman et al (2016) Database (preprint in BioRxiv)

27. Our seeds are largely
concepts linked to many
identifier systems
N identifiers per item
• Genes: 8
• Drugs: 18
• Diseases: 11
Facilitate
integration with
other key
knowledge bases

28. Planting Seeds for a Knowledge Commons

29. A Common Platform for knowledge integration and curation
29
Open data
Wikipedia(s)
Your Apps
Here!
Your Apps
Here!
Your Apps
Here!
Your Apps
Here!

30. Application #1 (of many)
Burgstaller et al (2016)

31. 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)

32. Application #2 Web Apollo Genome Browser
32Putman et al (2016)

33. Microbial Genetic Data

34. Stone Soups Harness Collaborative Spirit
• Programmers
• Data
Wikidata Workshop, International
Society for Biocuration
Geneva, Switzerland,
April 10-14 2016 !!!

35. Thanks!
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* First author on manuscript cited in this presentation
Ben Tim
Andra
Elvira
Sebastian
Some Gene Wiki team members
enjoying their best paper award
at SWAT4LS, Dec. 2015
Adapted logo
Su Laboratory at TSRI

37. Adding data automatically with a Bot
(1) Learn the API, use our library* perhaps..
(2) Use your Wikidata account to make tests
(3) Describe your project, request approval for bot user account
(4) If you need new properties, request approval
(5) Execute bot
(6) Pay attention to community reactions, they can block you if it goes
wrong..
*http://bitbucket.org/sulab/wikidatabots/

38. https://www.wikidata.org/wiki/Wikidata:Property_proposal/
Property proposal on wikidata
Proposal
Community discussion

39. Bot User: https://www.wikidata.org/wiki/User:ProteinBoxBot
• Describes bot activities
• Point of
communication with
community

40. https://www.wikidata.org/wiki/Wikidata:WikiProject_Molecular_biology
Coordination
area for a
domain