Gene Interaction/archive

Interaction Curation

Pipeline

semi-automatic curation with textpresso extracted sentences

• There are 2138 sentences (actually 2133 sentences) in the sourcefile /home/postgres/work/pgpopulation/genegeneinteraction/20091002-xiaodong/ggi_20091002
  • paper starts at WBPaper00028425, ends at WBPaper00035225

• .ace dumper at /home/acedb/xiaodong/gene_gene_interaction/dump_ggi_ace.pl
  • go to the directory and do: ./dump_ggi_ace.pl > some_file.ace

• Populate textpresso data in tazendra OA: done on 20110110 -X**

1. cd to directory on tazendra: /home/acedb/xiaodong/textpresso_ggi
2. mkdir directionay_name (eg 20110106)
3. cd directory_name (eg 20110106)
4. get Arun's result file (35225-35725.txt in the directory)
5. run script: ./populate_textpresso_ggi_to_OA.pl 20110106/35225-35725.txt WBPerson4793 > 20110106/35225-35725.pg (with first argument file_name as input file, and second argument WBPersonID, then output file)
6. after running, '20110106/35225-35725.pg' should be in '20111106' directory.

upload Gary and Chris RNAi-based interaction objects into OA

• Reading file created by Igor's script into aceDB
  • you can use the empty database by ssh -X citpub@spica.caltech.edu
  • then cd CitaceMirror
  • then type 'ts' to launch an empty acedb
• Dumping no-worry .ace file
• Then parse into OA
  • scp ace file to same directory as below
  • ssh acedb@tazendra.caltech.edu (directory xiaodong/interaction_ace_parsing)
  • To run : ./parse_ace_interaction_oa.pl gary_RNAi.ace WBPerson1823
  • where gary_RNAi.ace is the <inputfile>,the first argument, and WBPerson# is the second argument.