Difference between revisions of "OA-phenotype"
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Phenotype "WBPhenotype:0000456" Rescued_by_Transgene "asIs432248" Person_evidence "WBPerson712" | Phenotype "WBPhenotype:0000456" Rescued_by_Transgene "asIs432248" Person_evidence "WBPerson712" | ||
− | *legacy data- needs to be mapped to corresponding gene (app_wbgene)<br> | + | *legacy data- needs to be mapped to corresponding gene (app_wbgene)<br> '''while the table app_wbgene still exists, it is 1) not in the OA, 2) does not have WBGene objects, it has data in what looks like a bad format : WBGene00003883 (osm-1 (WBGene00003883)) or WBGene00000058 (acr-19). I don't know where this came from, but it seems bad. If you meant that we should dump whatever is in legacy pgids to existing app_wbgene, I don't see how since the legacy pgids are new, and the app_wbgene pgids are old and you can't add data to them without going to postgres directly. If you know where this data came from, let me know if it's good. If it's not good, let's back it up and get rid of the table -- J''' |
**.ace should be like | **.ace should be like | ||
Gene : "WBGene00003173" | Gene : "WBGene00003173" |
Revision as of 00:10, 29 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
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 what does constrain mean ? check_data button on OA ? so not in dumping script ? I can't find stuff like this in the dumping script. Unless it's a new thing, but I thought this was in the check_Data button. Did we ever wiki the dumping script ? -- J
- lines with mating_efficiency can be blank for phenotype (app_phenotype) Do you mean app_term ? This implies they can't be blank for other stuff, the script only does some stuff for pgids with data in app_term, does it already ever dump stuff when there isn't an app_term, and this new thing should join that, or is this the first time it will do that ? If we haven't gone the dumping script, we should, this seems like a pretty big change -- J
- .ace should look like the example is good -- J
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)
while the table app_wbgene still exists, it is 1) not in the OA, 2) does not have WBGene objects, it has data in what looks like a bad format : WBGene00003883 (osm-1 (WBGene00003883)) or WBGene00000058 (acr-19). I don't know where this came from, but it seems bad. If you meant that we should dump whatever is in legacy pgids to existing app_wbgene, I don't see how since the legacy pgids are new, and the app_wbgene pgids are old and you can't add data to them without going to postgres directly. If you know where this data came from, let me know if it's good. If it's not good, let's back it up and get rid of the table -- J- .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 |