User: Denise - Open Targets

Reputation:
4,360
Status:
Trusted
Location:
UK, Hinxton, EMBL-EBI
Website:
http://www.ebi.ac.uk/a...
Twitter:
@deniseOme
Scholar ID:
Google Scholar Page
Last seen:
1 day, 8 hours ago
Joined:
3 years, 6 months ago
Email:
r*******@yahoo.com

I'm currently leading the Outreach activities for Open Targets at EMBL-EBI with my love of genetic variants, genomes, user support, training, and communication in genomics and bioinformatics. Learning about early drug discovery and disease biology. Previously worked in Ensembl and Ensembl Genomes, GENCODE, EUCOMM and Pig Genome projects, with post-doctorate in human population genetics (at the Wellcome Trust Sanger Institute) and sex chromosome evolution (at the Australian National University).

Posts by Denise - Open Targets

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Comment: C: Open Targets, identifying targets for drug development in the treatment of disea
... The new GitHub for our project is called [Open Targets][1] now. There are links to our repo from the [Open Targets Platform][2] in every single footer of our pages. [1]: https://github.com/opentargets [2]: https://www.targetvalidation.org ...
written 26 days ago by Denise - Open Targets4.4k
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Answer: A: Comprehensive & integrated drug/target database?
... Have you tried the [Open Targets Platform][1]? At the moment we use ChEMBL as a drug-target database and are looking into incorporating DrugBank and PubChem soon. In addition to drug information from ChEMBL, we use genetics and genomics as evidence to associate targets with diseases. These come from ...
written 27 days ago by Denise - Open Targets4.4k
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Comment: C: How to visualize large VCF files
... No viral genomes in Ensembl Genomes. Check their [FAQ][1]. [1]: http://ensemblgenomes.org/node/30389 ...
written 4 weeks ago by Denise - Open Targets4.4k
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Answer: A: Synonym gene names have some ambiguity. Is it a curation issue or something biol
... You may want to bring this up with [UniProt][1] as the nomenclature used in Ensembl Plants seems to be coming from them. If you check these in TAIR, PIN5 is not listed as a synomym of PIN8, rather that [PIN8][2] acts together with [PIN5][3]. [1]: http://www.uniprot.org/uniprot/Q9LFP6 [2]: htt ...
written 8 weeks ago by Denise - Open Targets4.4k
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Answer: A: Number of Transcripts in GRCh38
... GENCODE calculates their stats taking into account the reference chromosomes only (check their [README_stats.txt][1] for the details), whereas the Ensembl provides the stats for reference chromosomes plus alternate sequences (haplotypes and patches). If you go to the the [Ensembl annotation page][ ...
written 8 weeks ago by Denise - Open Targets4.4k
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Answer: A: literature mining for genes and mutations
... You can try [BioMart][1] with all its different options of access (web, APIs, R package on bioconductor). The variation dataset of BioMart allows you to enter a list of Ensembl Gene IDs (you will need to convert to those, if your genes are not already in that format) as filters, than as attributes y ...
written 8 weeks ago by Denise - Open Targets4.4k
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Answer: A: Convert COSMIC ID to dbSNP id?
... The chances are your COSMIC IDs will not be convertable to rsIDs as the first are somatic mutations, not "neutral" genetic variants from dbSNP. There may be exceptions to this though. Unless the SNP had an rsID to begin with, followed by the observation that is implicated in cancer, it won't be cura ...
written 8 weeks ago by Denise - Open Targets4.4k
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Answer: A: How to get SNP identifiers from VCF file?
... Use the Ensembl [Variant Effect Predictor][1]. If your variant is known in the public database e.g. dbSNP you will get its rsID as VEP has an output option for co-located variants. VEP accepts [VCF][2] as an input file and you can run it through the [Ensembl REST API][3]. [1]: https://www.ensemb ...
written 8 weeks ago by Denise - Open Targets4.4k
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Answer: A: Looking for clinically validated anticancer drugs list
... You can use the [batch search][1] tool of [Open Targets][2]. Input your list of genes (either HGNC, UniProt IDs or Ensembl IDs) and get the drugs targeting those genes. You will get the drug (e.g. [CELECOXIB][3]), its clinical phase (e.g. IV), mechanism of action, and links to the original source of ...
written 8 weeks ago by Denise - Open Targets4.4k
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Comment: C: SNP Positioning on a Gene
... What do you mean by efficient way? What is the format of your list of SNPs? Is it a BED file? ...
written 9 weeks ago by Denise - Open Targets4.4k

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