1. MyGene.Info:
Gene Annotation as a Service - GAaaS
Chunlei Wu
cwu@scripps.edu
2011/07/16

2. A migration story for BioGPS
http://biogps.org

3. A migration story for BioGPS
http://biogps.org

4. A migration story for BioGPS
http://biogps.org

5. Gene-centric annotation data
http://biogps.org
A simple view:
Gene 1017 →Symbol: CDK2
→Ensembl: ENSG00000123374
→RefSeq: NM_001798
NM_052827
→Reporter: →U95A: 1792_g_at
1833_at
→U133A: 211804_s_at
204252_at
211803_at

6. A real example:
Symbol
Name
Alias
Summary
Ensembl
Refseq
UniGene
Homologene
GO
UniProt
InterPro
PDB
Prosite
IPI
And many more…

7. Relational database solutions
Solution 1: “star” schema
Ensembl Table
GeneID EnsemblID
Reporter Table 1017 ENSG00000250560
GeneID Platform Reporter
1017 U95A 1792_s_at Master Table
1017 U95A 1833_at GeneID Symbol
1017 U133A 211804_s_at 1017 CDK2
1017 U133A 204252_at Refseq Table
1017 U133A 211803_at GeneID RefseqID
1017 NM_001798
1017 NM_052827

8. Relational database solutions
Solution 2: “weakly-typed” schema
Generic Data Table
ID Type Value Parent Root
1 GeneID 1017 NULL 1017
2 Symbol CDK2 1017 1017
3 Ensembl ENSG00000123374 1017 1017
4 RefSeq NM_001798 1017 1017
5 RefSeq NM_052827 1017 1017
6 Platform U95A 1017 1017
7 Platform U133A 1017 1017
8 Reporter 1792_g_at U95A 1017
9 Reporter 1833_at U95A 1017
10 Reporter 211804_s_at U133A 1017
11 Reporter 204252_at U133A 1017
12 Reporter 211803_at U133A 1017

9. “Document”-based database solution
CDK2
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”
]
}
}

10. What’s CouchDB
 Document-based (“schema-free”) database
 Index and query data in MapReduce fashion
using Javascript
 RESTful JSON API
 Bi-directional replicator
 Distributed

11. Load data into “CouchDB”

NCBI “gene_info” file
Create bare-bone
document for each gene

Appending more annotation to
“document” Gene “document”
“gene2refseq”
“gene2ensembl”
“u95a_annot”
“u133a_annot”
And more …
Easy to add append data type Easy to update incrementally

12. What’s behind Mygene.info

13. Gene Annotation as a Service
http://MyGene.Info
Gene annotation services go PUBLIC
Gene query service
http://mygene.info/query?q=<query>
Gene annotation service
http://mygene.info/gene/<geneid>

14. Gene Query Service
user query  matching gene IDs/symbols/names
(JSON output)
http://mygene.info/query?q=<query>
Examples:
http://mygene.info/query?q=cdk2
http://mygene.info/query?q=cdk2+AND+species:human
http://mygene.info/query?q=cdk?
http://mygene.info/query?q=p*
http://mygene.info/query?q=entrezgene:1017
http://mygene.info/query?q=ensemblgene:ENSG00000123374

15. Gene Annotation Service
gene id  full or filtered gene annotation object
(JSON output)
http://mygene.info/gene/<geneid>
Examples:
http://mygene.info/gene/1017
http://mygene.info/gene/ENSG00000123374
http://mygene.info/gene/1017?filter=name,symbol,summary
http://mygene.info/gene/1017?filter=name,symbol,refseq.rna
Species supported:
human
mouse
rat
fruitfly
nematode
zebrafish
thale cress
frog

16. Targeted use case:
Quickly build a gene-centric online resource without the need of maintaining
a local gene annotation database
Use it in a web application:
Server side
Making direct HTTP calls
Client side
Setup a server-side proxy
JSONP calls
Cross-domain AJAX calls via CORS (Cross-Origin Resource Sharing)
Demo and full documentation at
http://mygene.info
Source code: https://bitbucket.org/newgene/genedoc/src

17. Acknowledgement
Group members: GNF collaborators:
Andrew Su Camilo Orozco
Jon Huss
Ian MacLeod
Benjamin Good Past contributor:
Eric Clarke
Marc Leglise ISMB travel support
Funding and Support
(NIH grant: R01GM083924)
http://mygene.info