Expression Pattern

Expression Pattern

Tags currently used in Expr_pattern objects (based on WS221):

Laboratory Expr_pattern Pattern Life_stage Gene Antibody Subcellular_localization GO_term Western Transgene Protein_description In_Situ Author Anatomy_term Reporter_gene Picture Date Reference Expressed_in Antibody_info Protein Northern Clone Cell RT_PCR Strain Remark MovieURL Pseudogene Curated_by Sequence

Types of fields Juancarlos can implement:

   * text : text
   * bigtext : text box expanded
   * dropdown : few values
   * ontology : controlled vocabulary 
   * multiontology / multidropdown : allows multiple values
   * toggle : on / off

OA interface

Tab1

• Pgdbid -- postgres database ID, generates automatically upon entry.
• Expr_pattern -- same as in interaction
  • no Expr_pattern ID is generated by clicking on 'new'. when 'duplicate', the ID from old entry will be in the field, but need to be deleted in order to get an new ID.
  • Expr_pattern ID should be assigned by cronjob daily at 4 am. start assigning with Expr10001
• Reference -- multiontology on paper WBPaperID - Daniela add wish list for term info. Juancarlos I am still thinking on what I would like to see displayed. Probably not much but it will be clear later on.
• Gene -- ontology on genes WBGeneID - show WBID, locus, and synonym in term info as in GO OA
• Anatomy term - multiontology. Controlled vocabulary found here: https://github.com/raymond91125/Wao/raw/master/WBbt.obo (same as in Picture OA). We need to have 3 different Anatomy term boxes, one for the Partial, one for the certain and one for the uncertain Qualifiers. We also have to think on how to inplement the text options for each anatomy term. normally the text would go for the parial qualifiers.
• GO_term - multiontology of GO_Term like gop_goid.
• Subcellular_localization - bigtext, details on subcellular localization.
• Life_stage - multiontology like in the phenotype OA and picture OA

Tab2

• Type - multidropdown select from: Antibody, Reporter_gene, In_situ, RT_PCR, Northern, Western but this is not possible because we have text associated to those values. For J, would be ideal to have a dropdown and once we choose from the dropdown we should have a text box associated with it

• Antibody -- bigtext " this tag was used 462 times and has text associated -> not possible just to toggle Call this Antibody Text or Antibody Type or Antibody Method so that the antibody objects below can be just 'Antibody' ? -- J
• Reporter_gene -- bigtext " this tag was used 7273 times and has been used twice for the same object! -> We need a separator between lines. We will add lots of text and would be good to have that text split into parts. Details on reporter gene construct. Multiline Not sure what you mean by multiline, if you mean the .ace file should have the tags multiple times (yes)we'd have to decide what the separator would be, you'd type the separator manually, and we'd have the dumper split on it -- J yes, I thnk this is the way to go is to add a separator manually D okay, we've pretty much always used | so just use that to separate entries, and let me know when we write the dumper to split on | and print out data in different tags. -- J great, I'll use the pipe to separate entries. I put a note at the end of the wiki a reminder for you when you write the dumper
• In_situ -- bigtext " this tag was used 434 times and has always text -> not possible just to toggle
• RT_PCR -- bigtext " this tag was used 165 times has text associated -> not possible just to toggle
• Northern -- bigtext " this tag was used 347 times and has text or just Northern label -> not possible just to toggle
• Western -- bigtext " this tag was used 19 times and has always text -> not possible just to toggle

all those above are the values of "type" right ? right D From the Reporter_gene description, does this mean you need to add text to this dropdown ? Do you want a "type" dropdown and a "type text" bigtext ? yes, would be great to be able to select one of the above with a dropdown and, once selected have a bigtext box next to it D. Well, we can have a Type multidropdown, and a Type_text bigtext, but each of the types you pick in the multidropdown won't be associated with anything specific in the big block of bigtext. If you wanted to have associations, you'd have to pick RT_PCR and Antibody (for example) in the multidropdown then in the bigtext you'd have to type RT_PCR <some rtpcr text> | Antibody <some antibody text> using the pipe ( | ) as a divider to separate the different things. At this point there's no point in having a multidropdown because you're typing everything in the bigtext field anyway. If you want to do things this way, add a "Type_text" bigtext field. I would instead suggest that if you want a tag + text associated with each other, you get rid of "Type" and make a lot of toggle_text fields, one for each of the types, then you could just click the toggle and type the text. We should probably talk about this in person since I'm not sure how you were originally picturing it working - J We will talk in person but both your suggestions would work. Suggestion 1 to have "Type_text" bigtext field and suggestion 2 to click the toggle and type the text. The final thing I want to have dumped in the .ace file is e.g. Northern "text" or In_situ "text". as long as we achieve that it does not make any difference :) D

We will have a multidropdown on the values above AND we will have bigtext fields for each of the values above. D&J decided this on March 21

• Picture Multiontology on Picture
• Picture flag toggle notify picture person with a cronjob every 2 weeks

notify picture person with a chronjob when when there is a new picture to curate Notify how ? -- J I put that note for myself but in the long run would be good to have a way to notify other curators when there is a new object they should curate. For the Expr_pattern OA this applies to Picture, transgene and antibody D It's still unclear to me how curators should get notified that there's a new value. We should probably talk about this. If this is something that "would be nice, but isn't important" but is still necessary for this field to exist, then okay, we don't have to talk about it. But if it turns out that we set it up in a way that won't work, I'm not going to want to talk about it after all the code's done and rewrite the code. Of course, we're not doing anything yet, we're just talking about how we will do this _eventually_ so there's no huge rush to talk about it -- J. Again, it will be best to talk in person about it but I think we could set up something like a "New object cgi" so that once that I see a new antibody that needs to be annotated I fill in a field and it generates a form that keeps track on the new objects that need attention. Hard to explain in a written form. Karen showed me something similar for phenotypes e.g. http://tazendra.caltech.edu/~postgres/cgi-bin/new_objects.cgi. We will see it 'live' the first time you step by. We set up flagging for Picture, Antibody and Transgene and the persons responsible for those data types are notified with a cronjob every 2 weeks. we will see with time if cronjob should be more frequent.

• Antibody_info -- multiontology on antibodies
• Antibody flag toggle -> notify antibody person with a cronjob every 2 weeks
• pattern bigtext, details on tissue distribution. Multiline
• remark bigtext, if any comments required. Multiline
• transgene multiontology on transgenes.
• Transgene flag toggle -> notify transgene person with a cronjob every 2 weeks
• Curator - Multiontology on people
• No dump - Toggle

Tab3

• Protein_description - text (30 objects)
• Clone - multiontology on clones (341 objects) (when OA is in place discuss with Chris on the clone class). Is there a better place to get clones than http://textpresso-dev.caltech.edu/gsa/worm/known_entities/Clone?

Clone and Strain lists could taken from spica from /home/citpub/arun/wb_entities/known_entities this lists are kept updated with what is in acedb daily using the following cronjob: 06 23 * * * cd /home/citpub/arun/wb_entities; ./01getEntities.pl

• Strain - multiontology on strains (812 objects). is there a better place to take the strain list then http://textpresso-dev.caltech.edu/gsa/worm/known_entities/Strain?

Clone and Strain lists could take from spica from /home/citpub/arun/wb_entities/known_entities this lists are kept updated with what is in acedb daily using the following cronjob: 06 23 * * * cd /home/citpub/arun/wb_entities; ./01getEntities.pl

• Cell - multiontology on anatomy terms (26 objects)-> when this is live consolidate these objects with the Anatomy_term field
• Sequence - text (13 objects) F54E2 2x (clone), R05D8 2x (clone), Y38B5A (clone), "Z28375" -C "EMBL Z28375" (sequence), "Z28376" -C "EMBL Z28376" (sequence), "Z28377" -C "EMBL Z28377" (sequence), R11H6 (clone), Y40H4A (clone), U14525, C47G2 (clone), Z32673 (sequence). We should consolidate these objects with Clones or Genes not sure what this consolidation means -- J. We will keep these objects as text in the beginning (this is to parse into old Expr_pattern data) but Wen and I have to find a way to get rid of this category in the long run and merge the Sequence with the clone, when possible. D okay, we're not working on this OA for a while yet, so if that gives you time to clean up this data, that'd be good. otherwise we can do it down the line -- J for the moment we will leave the text field and see how it goes. If I manage to clean it up before I'll tell you
• MovieURL(32 objects) text ? -- J yes D
• Laboratory - ontology (17 objects) There's an ontology of laboratories used for 3 OAs, if you want to use that. The labs are not updated though, so if you want to use "new" labs, text is fine -- J great, then we can use the laboratory ontology D I've changed the type to ontology, if you want multiontology, go ahead and change it -- J ontology is good. No values with multiple labs found so far
• Author - Multiontology on people
• Date - text (2617 objects)
• Curated_by - text (6228 objects) Not Curator, meaning WBPerson ? The curator field is required already, but this is a different thing ? -- J. no, this is a legacy thing, the values are only Hinxton and Caltech. Wen would like to get rid of it evntually but for the moment we are keeping it there D ah, ok -- J

notes: In the future we will get rid of the following tags: CDS, Sequence, Pseudogene and Protein and we will propose a model change for that. We will also get rid of Protein_description, Cell, Cell_group.

Tags used only once that should be fixed

• Expressed_in - text 1 entry
• Protein - text 1 entry could be put in Protein_description
• Homol_homol tag is used in Chronograms -> talk to Wen
• Pseudogene - text (1 object)

Chronogram tags

Right_priority Localizome Show_up_strand GFF_source Width Picture Reporter_gene Reference Gene Allow_misalign GFF_feature Transgene Homol_homol Remark Strain Colour Curated_by

the script to get the tags (e.g. from ExprWS221.ace or from Chronograms.ace) was written by Yuling, is called get_tags.pl and is located under desktop/Varia_protocols/get_tags

We will not include Chronograms in Expr_OA anyway as they are one time large scale exp.

Notes

when J will write the dumper for Reporter_gene remember to split on | and print out data in different tags. Daniela check if this applies to other entries.

passw-less connection

if you want to login to a remote machine without entering the pssw every time cd ~/.ssh into your local machine

copy the file id_rsa.pub into the remote machine you want to connect to into ~/.ssh/authorized_keys. If there is no authorized_keys folder you can creat one.

Detailed instrucytions can be found here http://www.debian-administration.org/articles/152