Process term curation and Process curation

Process term OA

Fields are OA field name -- postgres table name -- .ace Tag --

TAB1

• Curator -- prt_curator -- dropdown
• WBbioprID -- prt_processid -- WBProcess -- (this field is required by the OA) auto-incremental based on new record dump as WBProcess:"WBbiopr:00000000" 8 digits
• Process name -- prt_processname -- Public_name -- .ace dump as Public_name -- text
• Summary -- prt_summary -- Summary -- big text
• Other_name -- prt_othername -- Other_name -- big text, values will be pipe separated (note that looking for a process term in an OA WBProcess field will autocomplete first on WBbioprID, then process name, then this field. If you don't want this field to trigger autocomplete, let me know)
• Related_process -- prt_relprocess -- Related_process -- XREF to WBProcess -multi-ontology field, autocomplete on Process Term OA objects.
• Remark -- prt_remark -- Remark -- big text
• Paper -- prt_paper -- Reference -- multi-ontology autocomplete on WBPaperID

dumper at /home/postgres/work/citace_upload/process/
package is get_process_ace.pm
script is use_process_package.pl

.ace dump constraints

the following must be true:

• Unique WBProcessID
• Unique Process name
• Curator not blank
• Process summary not blank

Process_curation OA

Fields are OA field name -- postgres table name -- .ace Tag --

TAB1

• Curator -- pro_curator -- dropdown
• Paper -- pro_paper -- Paper_evidence -- single ontology, autocomplete on WBPaperID; term info-WBProcess, Gene, GO terms (need to clear this w/ everyone)
• Process -- pro_process -- WBProcess -- single ontology (required field by OA) autocomplete (term and syn), store WBProcessID, term info, WBProcess ID, WBProcess, Summary, other_name, WBPaper
• GO_term -- pro_goid -- GO_term --pro_paper #evidence-- multi-ontology autocomplete (name and syn); term info -description
• Gene -- pro_wbgene -- pro_paper #evidence-- Gene -- multi-ontology, autocomplete (public_name); term info-name, WBGeneID, WBProcess, WBPaper
• Phenotype -- pro_phenotype -- Phenotype --pro_paper #evidence-- multi-ontology, autocomplete (name and syn); term info -description
• Molecule -- pro_molecule -- Molecule -- pro_paper #evidence -- multi-ontology autocomplete (name and syn);term info-molecule ID, name, syn
• Sentence --pro_sentid--Sentence from http://131.215.52.209/karen/rank_paper_fullpaper_filtered (concatenate sentences for each paper keyed off WBPaper and MolID, with terminfo showing combined sentences- start each line with paper section, duplicate sentences for the same key get hashed out, WBPaper is added to pro_paper, curator 'Yuling' populates pro_cur)
• False positive --pro_falsepositive--toggle

TAB2

• Anatomy_term -- pro_anatomy -- Anatomy_term -- pro_paper #evidence-- multi-ontology autocomplete on name; term info- name, WBbt ID, store ID
• Life_stage -- pro_lifestage -- Life_stage -- pro_paper #evidence-- multi-ontology autocomplete on name; term info- name, store Life_stage ID
• Taxon -- pro_taxon-- NCBITaxonomyID -- multi-ontology of NCBITaxonomy ID, autocomplete on species name
• Expression_cluster -- pro_exprcluster -- Expression_cluster -- pro_paper #evidence-- multi-ontology
• Human_disease -- pro_humdisease -- text -- not in the model-- multi-ontology autocomplete on name and synonym text until file is ready for obo_ table

TAB3

• Picture -- pro_picture -- Picture -- pro_paper #evidence-- multi-ontology from picture OA table autocomplete on WBPaperID; term info -WBPicture, description, expr. I remember we talked about this field, but not what we said, you'll be doing curation to pictures from here instead of picture curation adding processes ? -- J Yes --K
• Movie -- pro_movie -- Movie -- pro_paper #evidence-- text -- until your file is ready for obo_ table
• Pathway -- pro_pathwaydb -- dump the same way it is dumped for Interaction bigtext -- until file is ready for obo_ table, see http://wiki.wormbase.org/index.php/Gene_Interaction#Instructions_on_How_to_Use_the_New_OA for how to enter data.

dumper at /home/postgres/work/citace_upload/process/
package is get_process_curation_ace.pm
script is use_process_curation_package.pl

20120916 Changes to Process_curation - adding in Textpresso sentences for molecul Changes to the OA

• add Sentence Field
• add False positive for Michael (Textpresso)
• uploading of sentences from textpresso http://131.215.52.209/karen/rank_paper_fullpaper_filtered
• script will load new sentences (skips any paper-molecule that already exists) when launched manually (this is not on a cron job)

Changes to the dumper module to not dump lines where curator is Yuling or the line is false positive: from :

 if ( $flag eq 'all' ) { $result = $dbh->prepare( "SELECT * FROM pro_process;" ); }
   else {  $result = $dbh->prepare( "SELECT * FROM pro_process WHERE pro_process ~ '$flag';" ); }

to :

  if ( $flag eq 'all' ) { $result = $dbh->prepare( "SELECT * FROM pro_process WHERE joinkey NOT IN (SELECT joinkey FROM pro_falsepositive) AND joinkey NOT IN (SELECT joinkey FROM pro_curator WHERE pro_curator = 'WBPerson11187');" ); }
    else {  $result = $dbh->prepare( "SELECT * FROM pro_process WHERE pro_process ~ '$flag' AND joinkey NOT IN (SELECT joinkey FROM pro_falsepositive) AND joinkey NOT IN (SELECT joinkey FROM pro_curator WHERE pro_curator = 'WBPerson11187');" ); }