ebi is an outstation of the european molecular biology laboratory. chebi: the story so far paula de...

EBI is an Outstation of the European Molecular Biology Laboratory.

ChEBI: The story so far

Paula de Matos

ChEBI: The story so far2

Private Data Public Data


The state of affairs of bioinformatics in 2002

• Bioinformatics is booming

• Human Genome sequence rough draft published June 2000

• Free resources and free data


A different story for chemoinformatics

• Private data and private software


Too hard to solve… lets put our head in the sand


Bioinformatics data too large to keep track of chemical compounds

• 100000 Protein entries in SwissProt (2002)

• 20 million entries in EMBL Database (2002)

• Small databases unable to keep track

• ENZYME resources ~ 3500 enzymatic reactions


New initiatives start up

• PubChem• Chemical repository, millions of entries, focus on screening

assays

• ChEBI • Manually annotated database, nomenclature reference and

compound database, tens of thousands of entries


Principles of foundation

• December 2002 email exchanges within the EBI to address the issue of chemistry

• Three principles outlined

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“Nothing held in the database must be proprietary or derived from a proprietary source that would limit its free distribution/availability to anyone.”


“Every data item in the database should be fully traceable and explicitly referenced to the original source/version.”


“Although the EBI will provide a web interface, the entirety of the data should be available to all without constraint as, for example, SQL table dumps, ASCII tables, and XML (e.g. DAML+OIL)”


We make a start using existing resources

• Integrate three resources• KEGG Compound• IntEnz • Chemical Ontology

• Annotation starts summer 2003• Focus on nomenclature

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Our first release was modest but it was a start

• 21 July 2004

• 2783 annotated entities

• Data:• ChEBI Name, ChEBI Id• IUPAC Names, Synonyms• Formula• Cross-references20

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We introduce structures - Sep 2005

• Molfiles

• InChI (IUPAC International Chemical Identifier)

• SMILES (Simplified Molecular Input Line Entry System)

• Image (PNG)

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Marvin in ChEBI


We start editing the chemical ontology – Dec 2005

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Internationalisation of web pages – March 2006


Internationalisation of data – Feb 2008

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Web Services - Oct 2006

• Programmatic access to a ChEBI entry• SOAP based Java implementation

• Clients currently available in Java and perl

• Four methods with which to access data• getLiteEntity • getCompleteEntity• getOntologyParents • getOntologyChildren

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Automated Cross References – Aug 2007

Current Databases:UniProtKB, Reactome, BioModels, IntAct, SABIO-RK, PubChem and ArrayExpress

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Chemical Structure Searching – May 2008


After all this, where are we?


Annotation is linear

ChEBI Data Growth

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Releases in month and year

Nu

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Number of web hits grows

• Total pure entry hits in April: 42,612 / 273,219• Total web services hits in April: 88,226 • Web hits for 2007:


Diversity of users

Constant challenge of balancing our users' varied interests.


Our positives

• Nomenclature database

• Manually annotated data

• Attention to detail

• Free and accessible

• Loyal users


Our not so positives

• Size for some people

• Not well integrated into other bioinformatics resources

• Community interaction

• No software publicly available to manipulate the database


Involve the community

• Create a submission web based tool• Users can easily submit their entities on a one to one basis• Also allowing bulk submission from other resources.


Improvements to data depth

• Addition of more Xrefs: PDB, MACIE ???

• Addition of more chemical attributes? What chemical attributes?

• Text mining projects to extract relevant chemical information from patents, journals• European Patent Office


Going Open Source

• Commercial software packages will be replaced with Open Source

• Long term goal: allow people to create a free local instance of ChEBI

• Distribution of data in useful formats: CML, SDF


Proposed changes to the ontology

• New relationships• “Is disjoint from”

molecular entities

organic molecular entities

inorganic molecular entities

organic ions


Is alloprote of

succinate(2−)CHEBI:30031

succinic acid CHEBI:15741

Is alloprote of


Has biological role and Has application

Has biological role


• Currently working with the Swiss Institute of Bioinformatics building a database of biochemical reactions called Rhea

• All reactions mapped to ChEBI

Encourage use of ChEBI nomenclature

CHEBI:15422

C10H16N5O13P3

CHEBI:16027

C10H14N5O7PCHEBI:16761

C10H15N5O10P2

EC 2.7.4.3“ATP + AMP = 2 ADP”


Acknowledgements

• ChEBI Team• Paula de Matos, Kirill

Degtyarenko, Marcus Ennis, Janna Hastings, Christoph Steinbeck

• Alumni • Michael Darsow, Mickael Guedj,

Alan McNaught, Martin Zbinden

• ChEBI supporters• Rolf Apweiler, Michael

Ashburner, Henning Hermjakob, Janet Thornton

• IntEnz Team• Rafael Alcantara, Volker Ast,

Kristian Axelsen, Anne Morgat

• EPO Collaborators• Helene Courrier, Stephane

Nauche, Jeremy Parsons

• Database supporters• ArrayExpress, IntAct,

Reactome, SABIO-RK, RSC, GO, RESID etc…


Discussion Points

Data Depth

New Relationships Encourage Nomenclature

Community

ebi is an outstation of the european molecular biology laboratory. chebi: the story so far paula de...

Documents

fara different story

entries chebi

chebi entrysoap

screening assays chebi

chebi idiupac names

annotated database

chemoinformaticsprivate

farbioinformatics data