MyGene.info: Gene Annotation Query as a Service talk at ISMB/BOSC 2013

1. MyGene.info
Chunlei Wu, Ph.D.
The Scripps Research Institute
La Jolla, CA, USA
BOSC 2013
July 20, 2013
- Making Elastic Gene API

2. Being “Elastic“
●
Fast
●
Always ON
●
Up-to-date
●
Scalable
●
Extensible

3. Common procedure for gene data retrieval
Entrez
Ensembl
UniProt
Internal gene object
Data sources Data parsing
update regularly
...

4. Common procedure for gene data retrieval
Entrez
Ensembl
UniProt
Internal gene object
Data sources Data parsing
update regularly
As A Service?
...
Common procedure for gene data retrieval
Entrez
Ensembl
UniProt
Internal gene object
Data sources Data parsing
update regularly
As A Service?
...

5. Working model - 1
Entrez
Ensembl
UniProt
Data sources
Merging
Query Engine
User queries
...

6. Working model - 1
Entrez
Ensembl
UniProt
Data sources
Merging
Query Engine
...
{
“entrezgene“: 1017
}
{
“uniprot“: “P24941”
}
A dummy merging example:
{
“ensemblgene“:
“ENSG00000123374”
}
{
“entrezgene“: 1017,
“ensemblgene“:
“ENSG00000123374”,
“uniprot“: “P24941”
}

7. Gene object in noSQL database
“key” “document”
1017: {
“Symbol”: “CDK2”,
“Ensembl”: “ENSG00000123374”,
“RefSeq”: [
“NM_001798”,
“NM_052827”
],
“Reporter”: {
“U95A”: [
“1792_g_at”,
“1833_at”
],
“U133A”:[
“211804_s_at”,
“2045252_at”,
“211803_at”
]
}
}

8. Syncing from data-hub to query instance
Merging
Entrez
Ensembl
UniProt
Data sources
...
Query Engine
User queries
Public data hub
Public query instance

9. Syncing from data-hub to query instances
Merging
Entrez
Ensembl
UniProt
Data sources
...
Query Engine
User queries
Public data hub
Public query instance

10. Public query instance
http://MyGene.info
(currently v2 API, two endpoints)
http://MyGene.info/v2/query?q=<query>
any query term(s)
matching gene hits
http://MyGene.info/v2/gene/<geneid>
gene id(s)
matching gene objects

11. Public query instance
●
Support ALL species, from NCBI (>12K species, >13M genes)
●
>40 annotation fields and expanding
●
Weekly-updated
●
Flexible query interface
●
Simple queries
●
Fielded queries
●
Wildcard queries
●
Genomic interval queries
●
Species filter
●
Returning fields filter
●
Support batch queries, JSONP, CORS
●
Committed for long-term availability
?q=cdk2
?q=symbol:cdk2
?q=cdk*
?q=chr1:1-100,000&species=human
?q=cdk2&species=mouse,rat
?q=cdk2&fields=symbol,homologene
http://MyGene.info

12. Public query instance
High-performance host (serving ~500K requests/day)
http://MyGene.info

13. Public query instance
MyGene.py - Python wrapper
https://pypi.python.org/pypi/mygene
Third-party packages
pip install mygene

14. Public query instance
MyGene.autocomplete
- Gene query autocomplete widget
https://bitbucket.org/sulab/mygene.autocomplete
Third-party packages

15. Public query instance
MyGene.autocomplete
- Gene query autocomplete widget
https://bitbucket.org/sulab/mygene.autocomplete
Third-party packages

16. Working model – 2
Entrez
Ensembl
UniProt
Data sources
Merging
Query Engine
User queriesMerging 1
Merging 2
Merging 3
Query Engine
Query Engine
...

17. Syncing from data-hub to query instances
Merging
Entrez
Ensembl
UniProt
Data sources
...
Query Engine
User queries
Public data hub
User queries
Query Engine
Private data hub
Merging
Merging
Private query instancePublic query instance
Private 1
Private 2
...

18. Private query instance
●
Dedicated host
●
Same powerful query interface
●
Third-party packages still work
●
Public data still get sync-ed
●
Allow to merge private data

19. To reach us?
Questions on public query instance
or
interested in setting up your own private query instance?
Please let us know:
help@mygene.info

20. Code repositories
●
Web front-end
https://bitbucket.org/sulab/mygene.info
Apache 2 licensed
●
Data hub
https://bitbucket.org/sulab/mygene.hub
GPL v3 licensed

21. Acknowledgement
Funding and Support
R01GM083924
Sulab
Andrew Su
Benjamin Good
Max Nannis
Salvatore Loguercio
Katie Fisch
Tobias Meissner

24. Syncing from data-hub to query instances
Merging
Entrez
Ensembl
UniProt
Data sources
...
Query Engine
User queries
Public data hub
User queries
Query Engine
Private data hub
Merging
Merging
Private query instancePublic query instance
Private 1
Private 2
...

25. Private query instance
●
Same powerful query interface
●
Third-party packages still work
●
Public data get sync-ed
●
Allow to merge private dataPublic data hub
Query Engine
Private data hub
MergingMerging
Private query instance
Private 1
Private 2
...
Entrez
Ensembl
UniProt
Data sources
...