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. 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'''
+
'''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
**rescued_by_transgene - multi-ontology from transgene tables, autocomplete on transgene name
+
**(NEW FIELD) rescued by - multi-ontology from transgene tables, autocomplete on transgene name
**legacy information -  
+
**(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>
***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'''
+
'''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>
  
*ease of scoring - drop down list, with values  
+
**(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"
*male mating efficiency - drop down list with values  
+
**(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"                                     
*hermaphrodite mating efficiency - drop down list with values  
+
**(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"
Line 70: Line 74:
 
  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). 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'''
+
*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

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"


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(!)
    • .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