The Wu Lab

Build Connected Knowledge Base for Biomedical Discovery

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Three key areas we are focusing on:

Data Infrastructure

Build high-performance scalable biological data access APIs

Semantic Web

Connect distributed knowledge via Linked Data technology

Biomedical Discovery

Apply integrated Knowledge Base for biomedical discovery

BioThings APIs

We build a collection of high-performance biological APIs

MyGene.info

Gene Annotation Query as a Service
- High-performance
  
  Fast API access to update-to-date Gene annotations.
- Up-to-date
  
  Weekly updated gene annotations from over 30 sources.
Visit MyGene.info
- Pre-integrated
  
  Gene annotations for >20M genes (>17K species) are pre-integrated.
- Simple to use
  
  Just two end-points to retrieve annotations via Gene IDs or any query term.
MyVariant.info

Variant Annotation as a Service
- High-performance
  
  Fast API access to update-to-date human variant annotations..
- Up-to-date
  
  Monthly updated variant annotations from 18 sources.
Visit MyVariant.info
- Pre-integrated
  
  Variant annotations for >400M human variants are pre-integrated.
- Simple to use
  
  Just two end-points to retrieve annotations via HGVS IDs or any query term.
MyChem.info

The same high-performance BioThings API for chemicals and drugs
- High-performance
  
  Fast API access to update-to-date chemical/drug annotations..
- Up-to-date
  
  Monthly updated chemical/drug annotations over 10 sources.
Visit MyChem.info
- Pre-integrated
  
  Annotations for >90M chemicals/drugs are pre-integrated.
- Simple to use
  
  Just two end-points to retrieve annotations via InChIKey or any query term.

BioThings SDK

A Software Developement Kit to turn a data file to an API

See the tutorial and the docs (in-progres)

What's new

Data release 20200105 and the retirement of NCBI's Unigene

The latest data release for MyGene.info is out and the details on this new release can be found...

Update on MyGene Downtime

As some of you may have noticed, MyGene.info went down intermittently on September 11th...

How are BioThings APIs used and how frequently are they used?

To ensure that our efforts produce value to the biomedical research community, we often try to...

Staying up-to-date on BioThings

The BioThings APIs exist to make it easier for you to keep your data/resource/tool/(whatever you...

VAPr - A python package for efficient Variant Analysis and Prioritization

One of our pride points for being able to pool, standardize, and share gene, variant, and other...

Making functional inferences from evolutionarily constrained regions with Aminode

One of our pride points for being able to pool, standardize, and share gene, variant, and other...

View more news

Our Team

Chunlei Wu
@chunleiwu

Jiwen (Kevin) Xin

Staff Scientist

Ginger Tsueng
@GTsueng

Staff Scientist

Marco Alvarado

Research Programmer III

Xinghua (Jerry) Zhou

Research Programmer III

Research Programmer

Research Programmer

Intern

Research Programmer

Administrative Assistant

See lab alumni here

Join us

If you are passionate about Bioinformatics, Data Science, Semantic Web, Machine-learning and Genomics, you are welcome to contact us (cwu -at- scripps -dot- edu) and we will find a suitable position (Scientist, Developer, PostDoc or Graduate Research Assistant) in our team.

Data Infrastructure

Semantic Web

Biomedical Discovery

MyGene.info

Gene Annotation Query as a Service

High-performance

Up-to-date

Pre-integrated

Simple to use

MyVariant.info

Variant Annotation as a Service

High-performance

Up-to-date

Pre-integrated

Simple to use

MyChem.info

The same high-performance BioThings API for chemicals and drugs

High-performance

Up-to-date

Pre-integrated

Simple to use

Data release 20200105 and the retirement of NCBI's Unigene

Update on MyGene Downtime

How are BioThings APIs used and how frequently are they used?

Staying up-to-date on BioThings

VAPr - A python package for efficient Variant Analysis and Prioritization

Making functional inferences from evolutionarily constrained regions with Aminode