Difference between revisions of "Pictures"

From WormBaseWiki
Jump to navigationJump to search
Line 105: Line 105:
* DB_info  -> links to entity in other database add following databases to database.ace
* DB_info  -> links to entity in other database add following databases to database.ace
==Molecule curation==
==Picture Data Model step by step explanation==
===Drug-phenotype curation===
===Drug-phenotype curation===

Revision as of 19:40, 29 September 2010

links to relevant pages
Caltech documentation

Picture Curation

The immediate goal of picture curation is to be able to obtain images of gene expression data from the literature and individual laboratories and display them in the WormBase gene expression page.

  • We want display images related to the temporal or spatial (e.g., tissue, subcellular, etc.) localization of any gene in a wild-type background with different data types
    • Reporter gene analysis
    • Antibody staining
    • In situ hybridization
    • RT-PCR
    • Western or Northern blot data


In the early phases of curation, pictures will be taken from open access journals (e.g. PLoS). During the process of PLoS image curation, other publishers will be contacted for obtaining copyright permissions.

The images should be saved and stored according to the following guidelines. The example shown below refers to a PLoS Biology paper but the rules of handling the pictures are universal and not "paper specific".

Pictures are downloaded in TIFF format from the original paper.


Pictures are saved with their original name in order to minimize editing from the curator. In this case the file is called “journal.pbio.0020352.g006”.

The file is saved in a directory named after the WB paper ID. E.g.: WBPaper00024505, meaning that picture “journal.pbio.0020352.g006” has been downloaded from WBPaper00024505.


These 2 numbers together WBPaper00024505_journal.pbio.0020352.g006 will be UNIQUE IDENTIFIERS of the object, that we call Picture object 1 (WBPicture000000001). The ID WBPicture000000001 will be the NAME of the object in the Picture Data Model.

The path WBPaper00024505_journal.pbio.0020352.g006 will define the SOURCE of the object in the Picture Data Model.

Now look at the picture above: In our WormBase expression pattern page we don’t want to display the whole picture because it contains information not pertinent to the expression data. We therefore need to CROP the 2 pictures depicting expression of the gene in the Wild Type. We want to have only panel B and F.

Each panel is cropped from the original picture in Photoshop and the files are saved as “journal.pbio.0020352.g006_B” “journal.pbio.0020352.g006_F” in the same directory as before: WBPaper00024505


These will be respectively Picture object 2(WBPicture000000002) and Picture object 3 (WBPicture000000003).

To summarize till now:

Picture object 1: WBPicture000000001: WBPaper00024505_ journal.pbio.0020352.g006

Picture object 2 WBPicture000000002: WBPaper00024505_ journal.pbio.0020352.g006_B

Picture object 3: WBPicture000000003: WBPaper00024505_ journal.pbio.0020352.g006_F

where WBPicture000000001 corresponds to the NAME of the object in the picture data model and WBPaper00024505_ journal.pbio.0020352.g006 corresponds to the SOURCE of the object in the picture data model.

At the same time, the text file associated with the entire figure WBPicture000000001, is saved with the same name as the figure -journal.pbio.0020352.g006- with a .doc extension. In this way we can make sure which figure legend goes with which picture.


NB: The size of the original TIFF file varies from 1 to 20 MB (in the examples observed till now). In order to minimize the space, the cropped images will be converted into PNG files (100KB to 2MB). We anyway have the parental image for users access. Supplementary material is generally stored by journals as PDF files. The PDF is converted in TIFF for consistency.

Let's go one step further:

Picture object 1 is our PARENTAL IMAGE, we will display it only when the user will click on a “see original figure” link Picture Objects 2 and 3 are our Daughter Images, which will be displayed on the gene expression page. See mock page below for a visual example:


Picture Data Model Proposal


?Picture      Description ?Text
              Name ?Text
              Source ?Text
              Image_lineage Crop_picture ?Picture XREF Cropped_from
                            Cropped_from ?Picture XREF Crop_picture
              Pick_me_to_call Text Text
              Expr_pattern ?Expr_pattern XREF Picture
              RNAi ?RNAi XREF Picture
              Variation ?Variation XREF Picture
              Transgene ?Transgene XREF Picture
              Reference ? XREF Picture
              Remark ?Text #Evidence
  • Name-> MeSH UID
  • Public name -> common name in elegans literature
  • Synonym -> other names, how do we mine these from other DBs?
  • DB_info -> links to entity in other database add following databases to database.ace

Picture Data Model step by step explanation

Drug-phenotype curation

Molecules will be linked to genes based on their influence on gene activity altered by variation, overexpression, and RNAi-based knockdown.

Drug-gene interactions

Molecules will also be linked to genes through their influence on gene activity directly through gene regulation interactions.

Molecule databases

Molecule IDs will be provided, when available, for the following databases:

  • Database "NLM_MeSH" "UID"
  • Database "CTD" "ChemicalID"
  • Database "ChemIDplus" using the CasRN
  • Database "ChEBI" "CHEBI_ID"

Molecule list

Initially, we will be using MeSH UIDs, assigned by the NLM, as IDs for the molecules in our database. Due to the more comprehensive coverage of the NLM molecules, and the fact that it is more stably funded, this source was thought to be a good starting point for this project. The list we are starting with is a pared down list of molecules from the NLM, that was created by the Comparative Toxicogenomic Database (CTD), which contains over 130,000 terms. For each term, this list contains a term name, CTD ID, MeSH UID, and where available CAS Registry Numbers. Using the CasRNs, we extracted the ChEBI ID from the Chemical Entities of Biological Interest database entity list, where it existed, along with any KEGG Compound accession number.

A sample molecule.ace record:

Molecule : "C009687"
Public_name "wortmannin"
Database "NLM_MeSH" "UID" "C009687"
Database "CTD"  "ChemicalID" "C009687"
Database "ChemIDplus"  "19545-26-7"
Database "ChEBI" "CHEBI_ID" "52289"