Difference between revisions of "OA-phenotype"

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**rescued_by_transgene - multi-ontology from transgene tables, autocomplete on transgene name
 
**rescued_by_transgene - multi-ontology from transgene tables, autocomplete on transgene name
 
**legacy information -  
 
**legacy information -  
***parse data from legacy data- all entries with [celegans] from file on tazendra and mangolassi at /home/acedb/work/allele_phenotype  
+
***parse data from legacy data- all entries with [celegans] from file on tazendra and mangolassi at /home/acedb/work/allele_phenotype '''This file ? /home/acedb/work/allele_phenotype/legacy_information.txt  There are no entries with "[celegans]"  Do you mean lines where it says --;"[C.elegansII]-- ?  What do you mean by parse ?  Enter everything in each line into a new app_ OA line with its own pgid ?  Or split on ";" and only enter stuff from the third column ?  or something else ? -- J'''
 
***each entry gets its own pgid  
 
***each entry gets its own pgid  
 
***add curation status (app_curation_status) of "down right disgusted" so lines that I have not touched do not get dumped.  
 
***add curation status (app_curation_status) of "down right disgusted" so lines that I have not touched do not get dumped.  
***make legacy data editable
+
***make legacy data editable '''text or bigtext ? -- J'''
 +
***'''what other fields ?  no app_name ?  you for app_curator ? -- J'''
  
 
*ease of scoring - drop down list, with values  
 
*ease of scoring - drop down list, with values  

Revision as of 23:56, 28 February 2012

package dump script

tazendra /home/acedb/work/allele_phenotype/use_package.pl

use_package.pl is a perl script that uses the perl module( ), to generate an error file and two .ace files (since May 2011)- one for phenotypes and one for molecule-phenotype.

Constraints:

  • does not dump record when value in Curation status is "down right disgusted", this acts as our no dump toggle
  • when there is no value for phenotype -this will stop non-curated NBP data from being dumped
  • will dump if phenotype is present regardless of curator

requested changes

5/17/2011

  • add a constraint - for rearrangement objects, dump all phenotype information except molecule values (molecule data should not be annotated for rearrangements so this is just a fail safe in case it does happen).
  • in addition to the varphene.ace output file, please output a separate file called mol_phene.ace, which contains:
  • molecule variation phenotype
  • molecule strain phenotype
  • molecule transgene phenotype

2/2012

I can't tell if all 5 of these are new fields, or just some. If they're all fields, are they all at the bottom of tab2, or just the first 2 fields ? Are you sure you want those field names, they're really long (which is fine by me, but will take up more space for you) -- J

  • Add fields to OA - add to TAB2 at the bottom in the following order
    • rescued_by_transgene - multi-ontology from transgene tables, autocomplete on transgene name
    • legacy information -
      • parse data from legacy data- all entries with [celegans] from file on tazendra and mangolassi at /home/acedb/work/allele_phenotype This file ? /home/acedb/work/allele_phenotype/legacy_information.txt There are no entries with "[celegans]" Do you mean lines where it says --;"[C.elegansII]-- ? What do you mean by parse ? Enter everything in each line into a new app_ OA line with its own pgid ? Or split on ";" and only enter stuff from the third column ? or something else ? -- J
      • each entry gets its own pgid
      • add curation status (app_curation_status) of "down right disgusted" so lines that I have not touched do not get dumped.
      • make legacy data editable text or bigtext ? -- J
      • what other fields ? no app_name ? you for app_curator ? -- J
  • ease of scoring - drop down list, with values
    • "ES0_Impossible_to_score", "ES1_Very_difficult_to_score", "ES2_Difficult_to_score", "ES3_Easy_to_score"
  • male mating efficiency - drop down list with values
    • "ME0_Mating_not_successful", "ME1_Mating_rarely_successful", "ME2_Mating_usually_successful", "ME3_Mating_always_successful"
  • hermaphrodite mating efficiency - drop down list with values
    • "HME0_Mating_not_successful", "HME1_Mating_rarely_successful", "HME2_Mating_usually_successful", "HME3_Mating_always_successful"


CHANGES TO DUMP SCRIPT

  • mating_efficiency
    • constrain lines with mating_efficiency values to be NOT NULL in app_curator, app_tempname (variation), app_person OR app_paper
    • lines with mating_efficiency can be blank for phenotype (app_phenotype)
    • .ace should look like
Variation : "WBVar00266499"
Male	"ME2_Mating_usually_successful"	Curator_confirmed	"WBPerson712"
Male	"ME2_Mating_usually_successful"	Person_evidence	"WBPerson261"


  • ease_of_scoring
    • .ace should be like
Variation : "WBVar00266499"
Species	"Caenorhabditis_elegans"
Phenotype	"WBPhenotype:0000456"	Curator_confirmed	"WBPerson712"
Phenotype	"WBPhenotype:0000456"	Person_evidence	"WBPerson261"
Phenotype	"WBPhenotype:0000456"	Remark	"touch-insensitive"	Curator_confirmed	"WBPerson712"
Phenotype	"WBPhenotype:0000456"	Remark	"touch-insensitive"	Person_evidence	"WBPerson261"
Phenotype	"WBPhenotype:0000456"	Ease_of_scoring	"ES2_Difficult_to_score"	Curator_confirmed	"WBPerson712"
Phenotype	"WBPhenotype:0000456"	Ease_of_scoring	"ES2_Difficult_to_score"	Person_evidence	"WBPerson261"
  • rescued_by_transgene
    • .ace should be like
Variation : "WBVar00266499"
Species	"Caenorhabditis_elegans"
Phenotype	"WBPhenotype:0000456"	Curator_confirmed	"WBPerson712"
Phenotype	"WBPhenotype:0000456"	Person_evidence	"WBPerson261"
Phenotype	"WBPhenotype:0000456"	Remark	"touch-insensitive"	Curator_confirmed	"WBPerson712"
Phenotype	"WBPhenotype:0000456"	Remark	"touch-insensitive"	Person_evidence	"WBPerson261"
Phenotype	"WBPhenotype:0000456"	Rescued_by_Transgene	"asIs432248"	Curator_confirmed	"WBPerson712"
Phenotype	"WBPhenotype:0000456"	Rescued_by_Transgene	"asIs432248"	Person_evidence	"WBPerson712"
  • legacy data- needs to be mapped to corresponding gene (app_wbgene)
    • .ace should be like
Gene :	"WBGene00003173"
Legacy_information	"[C.elegansII] u27amb : OA>30: e1494, e1852, u164amb etc. Cloned: 2 kb and 3 kb transcripts, transpliced to  SL1 and SL2, encode protein with Kunitztype serine protease inhibitor domains, EGF-like repeats.  mec-9:GFP expressed in touch  cells and PVD (3kb promoter) or more extensively (2kb promoter). [Chalfie and Au 1989\; Huang and Chalfie 1994\; TU]"

--kjy 23:33, 13 February 2012 (UTC)

Phenotype OA postgres tables

postgres tables
app_allele_status app_finished_hst app_not_hst app_range_hst
app_allele_status_hst app_func app_obj_remark app_range_start
app_anat_term app_func_hst app_obj_remark_hst app_range_start_hst
app_anat_term_hst app_genotype app_paper app_remark
app_caused_by app_genotype_hst app_paper_hst app_rnai_brief
app_caused_by_hst app_go_sug app_paper_remark app_rnai_brief_hst
app_caused_by_other app_go_sug_hst app_paper_remark_hst app_species
app_caused_by_other_hst app_haplo app_pat_effect app_species_hst
app_child_of app_haplo_hst app_pat_effect_hst app_strain
app_child_of_hst app_heat_degree app_penetrance app_strain_hst
app_cold_degree app_heat_degree_hst app_penetrance_hst app_suggested
app_cold_degree_hst app_heat_sens app_percent app_suggested_definition
app_cold_sens app_heat_sens_hst app_percent_hst app_suggested_definition_hst
app_cold_sens_hst app_intx_desc app_person app_suggested_hst
app_control_isolate app_intx_desc_hst app_person_hst app_sug_ref
app_control_isolate_hst app_laboratory app_phenotype app_sug_ref_hst
app_curation_status app_laboratory_hst app_phenotype_hst app_temperature
app_curation_status_hst app_lifestage app_phen_remark app_temperature_hst
app_curator app_lifestage_hst app_phen_remark_hst app_tempname
app_curator_hst app_mat_effect app_preparation_hst app_tempname_hst
app_delivered app_mat_effect_hst app_quality app_term
app_delivered_hst app_molecule app_quality_hst app_term_hst
app_entity app_molecule_hst app_quantity app_treatment
app_entity_hst app_nature app_quantity_hst app_treatment_hst
app_filereaddate app_nature_hst app_quantity_remark app_type
app_filereaddate_hst app_nbp app_quantity_remark_hst app_type_hst
app_finalname app_nbp_hst app_range_end app_wbgene
app_finalname_hst app_not app_range_end_hst app_wbgene_hst