OA-phenotype

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

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 - parsed from legacy data- all entries with [celegans] - deposited legacy info file on tazendra and mangolassi at /home/acedb/work/allele_phenotype. The legacy information needs to be loaded into the OA, all on new lines and with a concurrent status of "down right disgusted" so lines that I have not touched do not get dumped. As I work on the legacy information, I will be updating the information by deleting information that gets entered through the OA. Mary Ann wants a patch file with the updated legacy info for each gene touched, which means the legacy information will need to be mapped to each corresponding gene for the alleles touched.

• 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"

Add three more fields to dump script

• mating_efficiency
  • lines with mating_efficiency values do not need a value in phenotype (app_phenotype)
  • should have value in curator, variation, person, mating efficiency

• ease_of_scoring
• rescued_by_transgene

--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