User: Chris Maloney

gravatar for Chris Maloney
Chris Maloney310
Reputation:
310
Status:
New User
Location:
Bethesda, MD
Website:
http://chrismaloney.or...
Last seen:
7 months ago
Joined:
2 years, 5 months ago
Email:
v*******@gmail.com
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Google Scholar Page

Web developer at PMC/NCBI/NLM/NIH, bioinformatics student at JHU AAP, open-{source|access|science|data} advocate.

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Any answers or opinions I express here are mine personally, and not official in any way.

Posts by Chris Maloney

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Convert Pmids To Nihmsid And Pmcid Using Eutils
... I think perhaps you should look at the Public Access Compliance Monitor for what you are trying to do. You can get more information about it on the NIH Public Access page. As I commented on Neilfws' blog, we are coming out with a new web service for ID conversions - it should be deployed in a coup ...
written 7 months ago by Chris Maloney310
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Comment: C: How To Handle Transcripts Which Have No Peptide Sequence In Ensembl Perl Api?
... Small fix: you need to set $gene first, since it is used to get the value for $cdsseq: #!/usr/bin/env perl ... foreach my $gene_id (@gene_ids) { my $gene = $gene_adaptor->fetch_by_stable_id($gene_id); if ( defined ( my $cdsseq = $gene->canonical_transcript()->translateable_seq() ) ...
written 15 months ago by Chris Maloney310
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Comment: C: Accessing Geoprofiles Data Via Entrez
... Hi, Peter, I don't know why I didn't get notification of your comment, but I just noticed it. Yes, I reported it, and we are trying to improve the workflow so hopefully this won't happen in the future. ...
written 15 months ago by Chris Maloney310
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Answer: A: Accessing Geoprofiles Data Via Entrez
... I am not familiar with Biopython, but you can see the raw XML results from ESummary here (just open in your browser): http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmode=xml&version=2.0&db=geoprofiles&id=64663643. Reverse engineering a bit, it looks like biopython is tu ...
written 16 months ago by Chris Maloney310
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News: Looking For Feedback On The Json Output For Ncbi E-Utilities
... We're getting ready to add JSON output format to NCBI E-utilities, and would like to solicit community feedback. Please see the GitHub repository https://github.com/Klortho/Eutils-JSON for a very preliminary stylesheet that converts the existing XML format into JSON, as well as a few sample outpu ...
eutils ncbi news bioinformatics written 17 months ago by Chris Maloney310 • updated 17 months ago by Istvan Albert ♦♦ 39k
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Answer: A: What Is The Best Way To Interact Programmatically With Omim?
... As mentioned in another question, NCBI no longer serves OMIM data through efetch. The way to access OMIM now is through their API. ...
written 17 months ago by Chris Maloney310
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Comment: C: Identical Queries On Ncbi Gene And Protein Databases Returns Fewer Results From
... Nice response! Where'd you get that (excellent) list? Is it updated regularly? Who maintains it? Where does the underlying data come from? ...
written 18 months ago by Chris Maloney310
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Answer: A: Xml Returned Using Efetch Differs To That Downloaded From Query At Pubmed Websit
... I can add some evidence to support that it is the Ruby library not properly aggregating chunked results, and not a problem on the NCBI end. You can try this query out manually from the web interface: First fetch http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=retracti ...
written 21 months ago by Chris Maloney310
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Comment: C: What Does Agp Stand For?
... Oh, how poetic! Thanks a lot for the answer. ...
written 24 months ago by Chris Maloney310
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What Does Agp Stand For?
... The AGP format is defined here on the NCBI site. But I've searched high and low, and can't find out what the acronym stands for. ...
ncbi genome written 2.0 years ago by Chris Maloney310 • updated 5 months ago by Biostar ♦♦ 0

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