Difference between revisions of "Movie"

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Database : "RNAi"
Database : "RNAi"
Name "RNAi"
Name "RNAiDB"
URL "http://www.rnai.org"
URL "http://www.rnai.org"
URL_constructor "http://www.rnai.org/movies/%s"
URL_constructor "http://www.rnai.org/movies/%s"

Revision as of 08:31, 16 October 2013

Movie Curation

In October 2012 we have decided to generate a movie OA. There were 513 movies in acedb, all pertaining the RNAi class. We are going to generate the movie OA and import those objects. Files on tazendra /home/acedb/draciti/Movies

Movie Data Model


?Movie      Description ?Text
              Public_name UNIQUE Text
              Pick_me_to_call Text Text
                      RNAi ?RNAi XREF Movie
                      Variation ?Variation XREF Movie
                      Expr_pattern ?Expr_pattern XREF Movie
              Remark ?Text #Evidence 
              Reference ?Paper XREF Movie #added Oct2013 DR
              DB_INFO ?Database ?Database_field Text    #added Oct2013 DR         


  • Pgdbid -- no table -- postgres database ID, generates automatically upon entry.
  • WBMovie -> "mov_name" Generates automatically upon entry. WBMovie0000000001
  • Reference -> "mov_paper" WBPaperID paper ontology
  • Source -> "mov_source" text
  • Description -> "mov_description" bigtext
  • RNAi -> "mov_rnai" Text

There are 500 objects we currently have for movie/rnai are not in rnai OA but are stored in citace minus so we cannot import them as multiontology.

  • Expression pattern -> "mov_exprpattern" multiontology on expression patterns as in Picture OA
  • DB_INFO -> "mov_dbinfo" this field contains the DB_INFO including the Accession number for linking out to the url.
  • Variation -> "mov_variation" multiontology on variations like in phenotype OA tab1
  • Remark -> "mov_remark" text
  • Curator -> "mov_curator"


for DB_INFO tag Please make sure to enter in this format:

RNAi id OT/sp9h5-0101.mov
text space text space text

As of October 2013 the only database to which we are linking out is rnai.org. The Database info is hardcoded in the dumper to dump

Database : "RNAi"
Name	"RNAiDB"
URL	"http://www.rnai.org"
URL_constructor	"http://www.rnai.org/movies/%s"

We did not generate a mapping file as there is just one database.

.ace dumper

module /home/postgres/work/citace_upload/movie/get_movie_ace.pm

script /home/postgres/work/citace_upload/movie/use_movie_package.pl

The dumper on tazendra is here: /home/acedb/draciti/oa_movie_ace_dumper use_movie_package.pl@

When you decide to dump WBPaperIDs change the dumper

-D file for Citace Minus

Deposited on March 14th 2013. Filename: RNAiMovie.ace

Populating RNAi-Movie data

/home/postgres/work/pgpopulation/mov_movie/20121012_newOa/populate_movies_20121012.pl done in sandbox.

Spare_movies folder on canopus

located here /home/daniela/OICR/Movies were not in OA and probably refer to Zipperlain et al. Were discovered when we organized the movies in folders according to their WBPaperID and mapped to OA. Check to which RNAI object they match and add in OA. Checked on Oct 15th 2013. The movies were never made movie objects even pre-oa (check files to populate on tazendra /home/acedb/draciti/Movies). They were 'orphans' already then. Kept in the Spare_movies folder but no further action will be taken. DR

Future Directions

As of October 2012 movies came from 3 large scale studies

  • Fraser et al, 2000 -513 movies- (after correspondence with J Arhinger the movies were assigned to Zipperlen et al, 2001; WBPaper00004811). The Paper field in movie OA was populated on August 14 2013 through the RNAi mappings -DR.
  • Murray et al, 2012; WBPaper00040986 -321 movies
  • Piano et al, 2000
  • Piano et al 2002; WBPaper00005599

for the Piano Movies (stored at the rnai.org) database we have tried to obtain -and failed to have- the access to full movies from Chris Gunsalus at NYU. For this reason we requested a "database info-DB_INFO" tag to store the urls and link out directly - October 2013 DR

In the future if we are going to import more movies we have to make sure the file names will not overlap. To prevent this organized the folder on Canopus in the same way we have pictures. Done on october 11th 2013 DR

For this we should add in the ?Movie model the following tags

  • Reference ?Paper XREF Movie #added October 2013
  • Contact ?Person #Pending as not needed for now

Then we moved all the movie files in folders named after the WBPaerID, as it happens for pictures #done October 2013 DR

We already have a Paper field in OA and is dumping in .ace as per October 11th 2013 DR

Currently movies are stored here: /home/daniela/OICR

in the Movies folder