Specification for New Interactions and Phenotype FTP files

From SGD-Wiki
Revision as of 20:00, 16 July 2008 by Eurie (talk | contribs)
Jump to: navigation, search

SGD has released new interfaces to view physical and genetic interactions as well as new interfaces to view newly curated phenotype data. In order to provide these data in a convenient format to the scientific community, SGD has made two new FTP files to replace the current FTP files.

Phenotype

The new file is available in this directory:

ftp://genome-ftp.stanford.edu/pub/yeast/literature_curation/phenotype_data.tab

And will replace this file:

ftp://ftp.yeastgenome.org/yeast/literature_curation/phenotypes.tab

Time frame

The new phenotype_data.tab file is now available.

The old phenotypes.tab file will no longer be updated after July 14, 2008. It will be removed from the FTP directory October 31, 2008.

Column specifications

Column number Type of data Contents Required or Optional
1 Feature Name The feature name of the gene Required
2 Feature Type The feature type of the gene Required
3 Gene Name The standard name of the gene Optional
4 SGDID The SGDID of the gene Required
5 Reference PMID: #### SGD_REF: #### (separated by pipe)(one reference per row) SGD_REF Required, PMID optional
6 Experiment Type experiment_type (experiment_comment) experiment_type required, experiment_comment optional
7 Mutant Type mutant_type Required
8 Allele property_value (property_description) where property_type='Allele' Optional
9 Strain Background property_value where property_type='strain_background' Optional
10 Phenotype observable: qualifier Required
11 Chemical property_value (property_description) where property_type='Chemical_pending' or 'chebi_ontology'; multiple properties separated by pipes Optional
12 Condition property_value (property_description) where property_type='Condition'; multiple properties separated by pipes Optional
13 Details property_value (property_description) where property_type='Details'; multiple properties separated by pipes Optional
14 Reporter property_value (property_description) where property_type='Reporter' Optional

Interactions

The new file will be located in the following directory:

ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions_data.tab

And will replace this file:

ftp://ftp.yeastgenome.org/yeast/literature_curation/interactions.tab

Time frame

The new interactions_data.tab file is now available.

The old interactions.tab file will no longer be updated after July 14, 2008. It will be removed from the FTP directory October 31, 2008.

Column specifications

Column number Type of data Contents Required or Optional
1 Feature Name (Bait) The feature name of the gene used as the bait Required
2 Standard Gene Name (Bait) The standard gene name of the gene used as the bait Optional
3 Feature Name (Hit) The feature name of the gene that interacts with the bait Required
4 Standard Gene Name (Hit) The standard gene name of the gene that interacts with the bait Optional
5 Experiment Type A description of the experimental used to identify the interaction Required
6 Genetic or Physical Interaction Indicates whether the experimental method is a genetic or physical interaction Required
7 Source Lists the database source for the interaction Required
8 Manually curated or High-throughput Lists whether the interaction was manually curated from a publication or added as part of a high-throughput dataset Required
9 Notes Free text field that contains additional information about the interaction Optional
10 Phenotype Contains the phenotype of the interaction Optional
11 Reference Lists the identifiers for the reference as an SGDID (SGD_REF:) or a PubMed ID (PMID:) Required
12 Citation Lists the citation for the reference Required