Comments for I was lost but now I live here

Comment on An open letter to Oprah by Chewie

Chewie — Wed, 04 Nov 2009 21:49:47 +0000

That “concerned mother” is an idiot. I could not stomach to read her entire post, but I skimmed enough to catch the “wonderful god-given immune system” crap.

I suppose she doesn’t believe any of the numerous plagues that hit Europe in centuries past?

Comment on Scripts and hacks for curation by Heather Piwowar

Heather Piwowar — Mon, 19 Oct 2009 18:05:15 +0000

Hey Shirley. A similar question just came up on the BioNLP mailing list. PubMed Central might be able to get you part of the way there?

You can get free, open, programmatic access to lists of all PubMed papers cited by any paper in PubMed Central. Admittedly this limits the set in two ways (the cited papers need to have a PubMed ID, and the citing papers need to be in PubMed Central), but it can nonetheless be sufficient for many projects. Especially true as the number of papers in PubMed Central continues to rise. It also sets you up to filter the lists in all sorts of powerful ways, using the other Entrez tools.

eLink is the key to programmatic access for citations, just as with your SNP example.

For example, this URL returns a list of all five PubMed Central IDs that cite PubMed article ID 17375194 :
http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=17375194&db=pmc

This is the same list you see on the lower right “Cited by” list on the main PubMed page for the article:
http://www.ncbi.nlm.nih.gov/pubmed/17375194

I’ve done quite a bit of this sort of PubMed Central citation extraction in Python. I’ve been using an updated version of the EUtils python library and have some home-spun code as well (to be open source, but I haven’t posted it yet). If you are interested in more info or the code I’ve been using, let me know and I’d be glad to help (though with a bit of lag time, since I’m in the midst of moving to Vancouver Canada this week and am surrounded by moving boxes! )

Comment on An open letter to Oprah by Dr. Dubs

Dr. Dubs — Sat, 17 Oct 2009 06:24:37 +0000

Pharmacists support Shirley!

Comment on Contemplating careers: startups by Bioinformatics | Creating a company

Bioinformatics | Creating a company — Sun, 04 Oct 2009 17:07:49 +0000

[...] on a post by Shirley [...]

Comment on Corpus callosum: 1st edition of open science round-up by What would science look like if it were invented today – part II: knowledge structuring | fundscience.org

Wed, 30 Sep 2009 15:45:33 +0000

[...] shift in the way research is being done and communicated, towards what has come to be known as open science. As a side effect, commercial publishers would have to look for new things to publish, other than [...]

Comment on Incremental and continuous – a new paradigm for scientific publishing? by What would science look like if it were invented today – part II: knowledge structuring | fundscience.org

Wed, 30 Sep 2009 15:41:28 +0000

[...] information can be inserted at any time later, independent of press runs — some call this micropublication. For example, part I of this post has already been “published” on the blog, [...]

Comment on Jokes only a geek could love? by Dan

Dan — Mon, 21 Sep 2009 17:48:56 +0000

Heisenberg is pulled over for speeding:
“Do you know how fast you were going?” the police officer asks, incredulously. “No,” replies Heisenberg, “but I know exactly where I am!”

Comment on A community searching for a home by I declare social media sufficiently mainstream

I declare social media sufficiently mainstream — Fri, 18 Sep 2009 23:10:03 +0000

[...] (and that says more about me than anyone else). So I’ve been cautious online lately and searching for a home. Kind of silly to be cautious NOW when I have a tendency to write without a [...]

Comment on Scripts and hacks for curation by Firas

Firas — Fri, 18 Sep 2009 10:51:07 +0000

Biomedical Informatics grad student here. I am building hybrid NLP/machine learning classifiers for finding papers in PubMed in a domain that is very similar to yours. Once I’m done running the experiments, I want to release some of the code that I’ve written in open source. It’s not fancy, but I’m sure someone somewhere can find useful ways to add to it. It’s basically a web app written in CakePHP (like Ruby on Rails for PHP) that allows different kinds of queries to PubMed and then does bibliography management stuff, including ability to index based on NLP-extracted features.

I’d be more motivated to do start an open source project if other people are interested.

Comment on Scripts and hacks for curation by Chris Lasher

Chris Lasher — Fri, 18 Sep 2009 06:30:43 +0000

I’m fairly certain the LibX plugin http://libx.org/ hunts for DOIs on a page and provides annotations of them. (The VT LibX plugin, at least, usually puts a Virginia Tech logo by a DOI if it’s available from our library.) If you have the inclination to poke around their source code, it is open, and might provide you hints about how to make the improvements you imagined.