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{ Tag Archives } publishing

How to pull fields from MEDLINE the easy way

In response to this thread on FriendFeed… curl -s ‘http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=19614587&retmode=text&rettype=medline’|egrep ‘^(MH |DP )’ This will pull all the MeSH keywords and the date of publication from the article with PubMed ID 19614587. Stripping the field codes from the response is left as an exercise to the reader (but can be done trivially with a Unix [...]

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2009 10 08 Andrew Tips Comments (0)

Finding the dimensions of a PostScript image

If I have images in .ps or .eps format, how can I tell how big they are? i.e. how big would they print out at ‘natural’ size without any scaling? If they have a correct bounding box defined — more likely with EPS than PS files — this bit of Perl will show you the [...]

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2009 09 08 Andrew Tips Comments (3)

SESL 2009 day two

Semantic Enrichment of the Scientific Literature 2009 Tue 31 Mar: “Semantic Enrichment of the literature for the benefit of all users” (Monday’s notes are here) Missed the early morning session. I don’t work in pharma any more so it didn’t seem worth a 5:45am wake-up (unhelpful train times). Although apparently Eric Neumann’s talk on linked [...]

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2009 03 31 Andrew Events Comments (2)

Workshop notes — SESL 2009

Semantic Enrichment of the Scientific Literature 2009 Monday 30 Mar: “Reliable factual data from the literature based on ontological resources” Highlight of the morning session was Junichi Tsujii’s demo of the PathText system, which integrates manually-curated pathway information in CellDesigner or SBML format with text-mined relationships, and lets you browse the pathway maps and drill [...]

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2009 03 30 Andrew Events Comments (2)

What’s wrong with peer review

Michael Nielsen has posted a longish article entitled “Three myths about scientific peer review”. It’s thought-provoking reading and will strike a chord with most researchers. He uses various examples from 20th-century science and before to question our assumptions about how the system works (and how well). There’s apparently a follow-up about the future of peer [...]

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2009 01 09 Andrew Rants Comments (0)