Download from public repositories

From BioclipseWiki

Contents 1 Overview 2 Databases 2.1 Bioinformatics 2.1.1 DTP/NCI Molecular Targets 2.2 Chemoinformatics 2.2.1 Chemspider 2.2.2 NMRShiftDB 2.2.3 DTP/NCI chemical structures 2.2.4 DTP/NCI compound growth inhibition data 3 Services 3.1 WSDbFetch @ EBI 3.2 DTP/NCI Compound Services

Overview

This page aim to describe interesting public repositories for downloading data into Bioclipse, preferably via Web services.

Databases

Bioinformatics

DTP/NCI Molecular Targets

Characterization of NCI-60 set of human tumor cell lines. Includes extensive gene expression measurements via microarray.

URL: http://dtp.nci.nih.gov/mtargets/mt_index.html

Web Service: in progress (contact zaharevitz@dtpax2.ncifcrf.gov)

Chemoinformatics

Chemspider

Chemical structures, SMILES, InchI.

URL: http://www.chemspider.com

Web service: http://www.chemspider.com/Search.asmx

NMRShiftDB

Chemical Structures and assigned NMR spectra

URL: http://www.nmrshiftdb.org

Web service: http://nmrshiftdb.ice.mpg.de/axis/NMRShiftDB.wsdl

net.bioclipse.nmrshiftdb (part of speclipse feature) offers searches and downloads.

DTP/NCI chemical structures

~270K chemical structures collected by NCI

URL: http://dtp.nci.nih.gov/docs/3d_database/Structural_information/structural_data.html

Web service: in progress(contact zaharevitz@dtpax2.ncifcrf.gov)

DTP/NCI compound growth inhibition data

growth inhibition of ~45K compounds measured in the NCI-60 human tumor cell line set

URL: http://dtp.nci.nih.gov/docs/cancer/cancer_data.html

Web service: in progress(contact zaharevitz@dtpax2.ncifcrf.gov)

Services

WSDbFetch @ EBI

WSDbfetch allows you to retrieve entries from various up-to-date biological databases using entry identifiers or accession numbers.

• Nucleotide sequences: embl emblann emblcds emblcon emblsva refseq
• Protein sequences: uniprotkb uniref100 uniref50 uniref90 uniparc unisave refseqp
• Protein structures: pdb
• Patented protein sequences: epo_prt uspto_prt jpo_prt
• Literature: medline
• Specialized: genomereviews hgvbase interpro ipi

Webpage: http://www.ebi.ac.uk/Tools/webservices/services/dbfetch

DTP/NCI Compound Services

We are working to set this up and looking for people who are interested in helping us. The aim is to allow users editing a chemical structure in Bioclipse to:

• search for similar structures in the DTP compound set
• request a sample of the compound from the DTP repository (see http://dtp.nci.nih.gov/branches/dscb/repo_open.html )
• submit the compound for testing in the NCI-60 screen (see http://dtp.nci.nih.gov/docs/misc/common_files/submit_compounds.html)

Longer term we would like to develop data access, display, and analysis tools for researchers that submit compounds to DTP for testing. If interested contact zaharevitz@dtpax2.ncifcrf.gov