Difference between revisions of "OA-phenotype"
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====2/2012==== | ====2/2012==== | ||
− | '''I can't tell if all 5 of these are new fields, or just some. | + | '''I can't tell if all 5 of these are new fields, or just some.''' They are all new fields. <br> |
+ | '''If they're all fields, are they all at the bottom of tab2, or just the first 2 fields ?''' Yes, add them all to tab 2 bottom<br> | ||
+ | '''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''' Good point, I shortened them<br> | ||
*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 | ||
− | ** | + | **(NEW FIELD) rescued by - multi-ontology from transgene tables, autocomplete on transgene name |
− | **legacy | + | **(NEW FIELD) legacy info - parsed 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]-- ?''' yes<br> |
− | + | '''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''' take everything in quotes starting with the third column where there is "[C. elegansII], in some cases there are more semi-colons, these will need to be ignored after the third column<br> | |
***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 '''text or bigtext ? -- J''' | + | ***make legacy data editable '''text or bigtext ? -- J''' bigtext <br> |
− | ***'''what other fields ? no app_name ? you for app_curator ? -- J''' | + | ***'''what other fields ? no app_name ? you for app_curator ? -- J''' sure, me for app_curator<br> |
− | * | + | **(NEW FIELD) ES - drop down list, with values |
− | **"ES0_Impossible_to_score", "ES1_Very_difficult_to_score", "ES2_Difficult_to_score", "ES3_Easy_to_score" | + | ***"ES0_Impossible_to_score", "ES1_Very_difficult_to_score", "ES2_Difficult_to_score", "ES3_Easy_to_score" |
− | * | + | **(NEW FIELD) ME - drop down list with values |
− | **"ME0_Mating_not_successful", "ME1_Mating_rarely_successful", "ME2_Mating_usually_successful", "ME3_Mating_always_successful" | + | ***"ME0_Mating_not_successful", "ME1_Mating_rarely_successful", "ME2_Mating_usually_successful", "ME3_Mating_always_successful" |
− | * | + | **(NEW FIELD) HME - drop down list with values |
− | **"HME0_Mating_not_successful", "HME1_Mating_rarely_successful", "HME2_Mating_usually_successful", "HME3_Mating_always_successful" | + | ***"HME0_Mating_not_successful", "HME1_Mating_rarely_successful", "HME2_Mating_usually_successful", "HME3_Mating_always_successful" |
'''CHANGES TO DUMP SCRIPT''' | '''CHANGES TO DUMP SCRIPT''' | ||
*mating_efficiency | *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''' | + | **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''' https://bitbucket.org/kyook/ky_wbprojects/wiki/use_package.pl we did go over the dumping script, there are some constraints (rules? you probably have another term for this) that I thought were employed, see the bit bucket page. |
− | **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''' | + | |
+ | **lines with mating_efficiency can be blank for phenotype (app_phenotype) '''Do you mean app_term ?''' yes, sorry<br> '''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''' You are correct the script already has rules in it to not dump data when there is no phenotype (app_term); however, lines with mating efficiency values (ME and or HME) will need to escape that rule. I hope this is not a big change(!) | ||
+ | |||
**.ace should look like '''the example is good -- J''' | **.ace should look like '''the example is good -- J''' | ||
Variation : "WBVar00266499" | Variation : "WBVar00266499" | ||
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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> '''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). | + | *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.''' This is most likely from the Variation_gene.txt I create after each build so alleles can be mapped to genes. |
+ | |||
+ | '''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.''' no, you are correct that is not what I meant. | ||
+ | |||
+ | '''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''' if it isn't being used then yes, by all means we should get rid of it. Can you get rid of it on mangolassi so we can see what happens? As it is an app_wbgene table it is only looked at by the phenotype OA correct? | ||
+ | |||
**.ace should be like | **.ace should be like | ||
Gene : "WBGene00003173" | Gene : "WBGene00003173" |
Revision as of 01:25, 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. They are all new fields.
If they're all fields, are they all at the bottom of tab2, or just the first 2 fields ? Yes, add them all to tab 2 bottom
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 Good point, I shortened them
- Add fields to OA - add to TAB2 at the bottom in the following order
- (NEW FIELD) rescued by - multi-ontology from transgene tables, autocomplete on transgene name
- (NEW FIELD) legacy info - parsed 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]-- ? yes
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 take everything in quotes starting with the third column where there is "[C. elegansII], in some cases there are more semi-colons, these will need to be ignored after the third column
- 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 bigtext
- what other fields ? no app_name ? you for app_curator ? -- J sure, me for app_curator
- (NEW FIELD) ES - drop down list, with values
- "ES0_Impossible_to_score", "ES1_Very_difficult_to_score", "ES2_Difficult_to_score", "ES3_Easy_to_score"
- (NEW FIELD) ME - drop down list with values
- "ME0_Mating_not_successful", "ME1_Mating_rarely_successful", "ME2_Mating_usually_successful", "ME3_Mating_always_successful"
- (NEW FIELD) HME - drop down list with values
- "HME0_Mating_not_successful", "HME1_Mating_rarely_successful", "HME2_Mating_usually_successful", "HME3_Mating_always_successful"
- (NEW FIELD) ES - drop down list, with values
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 https://bitbucket.org/kyook/ky_wbprojects/wiki/use_package.pl we did go over the dumping script, there are some constraints (rules? you probably have another term for this) that I thought were employed, see the bit bucket page.
- lines with mating_efficiency can be blank for phenotype (app_phenotype) Do you mean app_term ? yes, sorry
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 You are correct the script already has rules in it to not dump data when there is no phenotype (app_term); however, lines with mating efficiency values (ME and or HME) will need to escape that rule. I hope this is not a big change(!)
- lines with mating_efficiency can be blank for phenotype (app_phenotype) Do you mean app_term ? yes, sorry
- .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. This is most likely from the Variation_gene.txt I create after each build so alleles can be mapped to genes.
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. no, you are correct that is not what I meant.
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 if it isn't being used then yes, by all means we should get rid of it. Can you get rid of it on mangolassi so we can see what happens? As it is an app_wbgene table it is only looked at by the phenotype OA correct?
- .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 |