/citationlookup

Citation Lookup Tool

Primary LanguagePHP

Citation Lookup Tool

The Citation Lookup Tool (CLT) is a PHP-based interface for converting manually entered citations into structured records from PubMed.

Business case

During their annual review cycle, faculty paste in blocks of citations from their CV's. In order to import these records into a VIVO profile, they first need to be validated (some publications have not even published) and, possibly, corrected.

However such submissions contain various features which make automated lookup challenging.

  • misspellings
  • formatting issues like line breaks in the middle of a citation
  • "meta" words (e.g., "In Process")
  • multiple citations in the same submission

Demo

How it currently works

User upload

User uploads a spreadsheet with the following columns: cwid, name, sequence, title, volume, number, page_end, page_start, pmid, eval_year, publication_full. The only field which is evaluated is publication_full; the cwid and name fields are merely used as a key. (Note that the remaining fields are a legacy of the Faculty Review Tool and are not assessed in any way.)

Pre-processing

Software pre-processes citations in the following ways:

  • separates out individual citations (in cases where multiple citations are in a single submission)
  • ignores premature line breaks so a given citation may be associated with no more than one citation
  • drops stop words
  • drops numbers from the start of citations (e.g., "54. Cancer and the...")

Parsing using AnyStyle.io

Parses the citations using the AnyStyle.io web service. For example, this record:

A molecular signature of tissues with pacemaker activity in the heart and upper urinary tract involves coexed hyperpolarization-activated cation and T-type Ca2+ channels. Hurtado R, Bub G, Herzlinger D. FASEB J. 2014 Feb;28(2):730-9. doi: 10.1096/fj.13-237289. Epub 2013 Nov 4.

Is converted into this:

Author: R, Hurtado and G, Bub and J, Herzlinger D.F.A.S.E.B.

Title: A molecular signature of tissues with pacemaker activity in the heart and upper urinary tract involves coexed hyperpolarization-activated cation and T-type Ca2+ channels

Type: incollection

Language: en

PubMed Search

Application constructs a query for PubMed which includes first two author names and the five longest words. For example, in the above example, the PubMed search would be: "Hurtado Bub hyperpolarization-activated pacemaker signature molecular."

PubMed returns one of the following for each record:

  • no PMID's
  • one PMID
  • two or more PMID's

Here is what the results look like: https://dl.dropboxusercontent.com/u/2014679/citationlookup.png)