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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

Approved model

///////////////////////////small molecule/chemical/drug ////////////////////////////
// ?Molecule
//  * metabolites: precursors, intermediates, or end products of a metabolic pathway
//  * monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats??
//  * chemicals/drugs
//  * minerals, ions, salts
?Molecule     Name ?Text
	       Public_name ?Text
	       Synonym ?Text
	       DB_info Database ?Database ?Database_field ?Accession_number 
               Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator 
	      Affects_phenotype_of 	Variation ?Variation  #Evidence
					Strain	?Strain	#Evidence
					Transgene ?Transgene #Evidence
					RNAi ?RNAi #Evidence

Corresponding changes in touched models

?Phenotype_info    Affected_by  Molecule  ?Molecule    #Evidence
?Gene_regulation  Regulator Molecule_regulator   ?Molecule  XREF  Gene_regulator  #Boolean 

Model elements

  • 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

Molecule curation

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"