User: Heather Piwowar

gravatar for Heather Piwowar
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380
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Vancouver, Canada
Website:
http://www.researchrem...
Last seen:
6 years ago
Joined:
7 years, 6 months ago
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Posts by Heather Piwowar

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Examples Of Full-Text Mining On The Pubmed Central Open Access Subset
... ok! yes, that was clear... thought it might be relevant because the code can be applied to an arbitrary and large subset of the PMC OA by changing the query parameters, and thereby help make your case that more is better. But I get it isn't what you want. Cheers. ...
written 6.1 years ago by Heather Piwowar380
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Answer: A: Examples Of Full-Text Mining On The Pubmed Central Open Access Subset
... I've done some NLP work that leveraged the OA PMC subset. The particular application below used only a subset of PMC OA papers -- those that matched given title/abstract keywords -- but is generally applicable to the whole subset. Using open access literature to guide full-text query formulation. ...
written 6.1 years ago by Heather Piwowar380
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Comment: C: Find All Genbank Submissions Associated With An Article Publication In 2005
... Neil, as a modification of #1 above, would it work if I started with the Nucleotide database ID and then link through to its PubMed IDs using dbfrom=nuccore&db=pubmed&id=NUCCOREID ?. Then I could eliminate from my list all NUCCOREIDs that don't lead to PMIDs with a 2005 PMID date. This ...
written 6.7 years ago by Heather Piwowar380
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Comment: C: Find All Genbank Submissions Associated With An Article Publication In 2005
... Thanks, Maximilian, your first paragraph is a very helpful clarification and consistent with my experience. Yes, pointers to some starting scripts would be great, if that is easy? ...
written 6.7 years ago by Heather Piwowar380
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Comment: C: Find All Genbank Submissions Associated With An Article Publication In 2005
... Thanks, Lars. I wasn't clear in my post originally... I'm actually looking for datasets with links to ANY AND ALL journal articles, so I don't think this approach will get me what I need. I tried to NOT "Unpublished"[Journal] but that doesn't work (and isn't ideal anyway) ...
written 6.7 years ago by Heather Piwowar380
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Find All Genbank Submissions Associated With An Article Publication In 2005
... Is there an easy way to query Genbank for all sequence submissions associated with ANY journal article published in 2005? So, all sequences that have a JOURNAL metadata line that includes "2005" (and ideally a real journal name and/or PMID) but without a related TITLE of Direct Submission. I'm int ...
genbank eutils retrieval written 6.7 years ago by Heather Piwowar380 • updated 4.3 years ago by cdsouthan1.7k
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Comment: C: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
... googling r-project works pretty well too ...
written 7.5 years ago by Heather Piwowar380
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Answer: A: What Are Some Good Free Bioinformatics And Computational Biology Books?
... I like the online book [?]Producing Open Source Software: How to Run a Successful Free Software Project[?]. Lots of other books are free when you raid friend's bookshelves, libraries (print and ebooks), and http://www.swaptree.com :) ETA: Just found some more free books at the [?]NCBI Bookshelf[?] ...
written 7.5 years ago by Heather Piwowar380
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Answer: A: Tagging Pubmed With Umls
... The Medline demo at Lingpipe might help: http://alias-i.com/lingpipe/demos/tutorial/medline/read-me.html and a specialized version, LingMed, at http://alias-i.com/lingpipe/web/sandbox.html I can't see a Lingpipe example of tagging with the UMLS per se, but you could probably make it work. Or, you c ...
written 7.5 years ago by Heather Piwowar380
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Comment: C: Tagging Pubmed With Umls
... Are you looking for tagged PubMed/Medline abstracts, or article full text? I can't tell from your question and comments. ...
written 7.5 years ago by Heather Piwowar380

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