Difference between revisions of "TAIR CCC"

Revision as of 16:58, 9 December 2010

This document is an outline of the Arabidopsis Textpresso for CCC pipeline for the initial trial run.

The trial run will be a search on all papers in the Textpresso for Arabidopsis corpus published in 2008.

Search results will be stored in three files:

1) all sentences returned by the search

2) sentences from papers already curated by TAIR for GO Cellular Component

3) sentences from papers not curated by TAIR for GO Cellular Component

Annotations can be made using an on-line curation form:

with two different outputs:

1) a three-column 'user submission' output

2) a standard GO Gene Association File (GAF) format

TAIR curator sends PDFs of papers to be included in the corpus to Textpresso (Michael) approximately every six months

Any additional papers for which TAIR does not have a PDF are downloaded by Textpresso team, if possible

@@ Line 35: / Line 35: @@
 *Any additional papers for which TAIR does not have a PDF are downloaded by Textpresso team, if possible
+====Textpresso Search Details====
+===Categories===
+*Search Arabidopsis corpus on:
+http://www.textpresso.org/arabidopsis/
+Using these four categories:
+) CCC assay terms
+) CCC cellular components
+) CCC verbs
+) genes (arabidopsis)
+'''Paths''' for categories on textpresso-dev.caltech.edu:
+/data2/data-processing/data/arabidopsis/Data/ontology/lexica
+) CCC assay terms
+) CCC cellular component
+) CCC verbs
+'''Juancarlos, can you fill in the exact path names here? --K'''
+'''Path''' name for arabidopsis genes on textpresso-dev.caltech.edu:
+) genes (arabidopsis)
+/data2/data-processing/data/arabidopsis/Data/ontology/lexica/genes_arabidopsis.0-gram
+'''Juancarlos, can you confirm that this is the path we used for genes (arabidopsis)? --K'''
 Back to [[Gene Ontology]]