OA-phenotype
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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
- 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
- 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 |