Difference between revisions of "OA-phenotype"
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Add fields to OA - add to TAB2 at the bottom in the following order | Add fields to OA - add to TAB2 at the bottom in the following order | ||
− | *rescued_by_transgene - | + | *rescued_by_transgene - multi-ontology from transgene tables, autocomplete on transgene name |
− | *legacy information - parsed from legacy data- all entries with [celegans] - | + | *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. |
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+ | *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 | Add three more fields to dump script |
Revision as of 01:57, 14 February 2012
Contents
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.
- 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 |