Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
biogrid_projectindex [2018/09/13 01:36]
biogridadmin
biogrid_projectindex [2018/09/13 01:47]
biogridadmin [Column Definitions]
Line 27: Line 27:
 === Additional Column Definitions (Repeating) === === Additional Column Definitions (Repeating) ===
 In addition to above, PROJECTINDEX files can contain any number of additional columns, depending on the project being represented. Since these columns may differ significantly from one project to the next, it's best to examine the project page within BioGRID for more detailed information about the project specific columns. Any additional columns will come in the following sets of 7 columns which are repeated N times for each unique dataset: In addition to above, PROJECTINDEX files can contain any number of additional columns, depending on the project being represented. Since these columns may differ significantly from one project to the next, it's best to examine the project page within BioGRID for more detailed information about the project specific columns. Any additional columns will come in the following sets of 7 columns which are repeated N times for each unique dataset:
 +
   - **<​COLUMN_NAME>​_values** - This column contains the values used on the web version for the corresponding column on our project pages. This will contain one or more values (separated by "​|"​) and are usually a type of classification or ontology reference.   - **<​COLUMN_NAME>​_values** - This column contains the values used on the web version for the corresponding column on our project pages. This will contain one or more values (separated by "​|"​) and are usually a type of classification or ontology reference.
   - **<​COLUMN_NAME>​_ids** - If the value entered up above also has an accompanying official id, this column will contain matching "​|"​ separate ID values associated with those in the <​COLUMN_NAME>​_values column. For example, if <​COLUMN_NAME>​_values contains Gene Ontology Terms, this column would contain corresponding Gene Ontology Term IDs. If not applicable, this column will contain "​-"​   - **<​COLUMN_NAME>​_ids** - If the value entered up above also has an accompanying official id, this column will contain matching "​|"​ separate ID values associated with those in the <​COLUMN_NAME>​_values column. For example, if <​COLUMN_NAME>​_values contains Gene Ontology Terms, this column would contain corresponding Gene Ontology Term IDs. If not applicable, this column will contain "​-"​
-  - **<​COLUMN_NAME>​_tags** - Tags are another level of associated qualifications on an original ​V +  - **<​COLUMN_NAME>​_tags** - Tags are another level of associated qualifications on an original ​value. A use for this column might be to further subclassify a major category or to simply add-on more information about a mapped value. If not applicable, this column will contain "​-"​ 
-  - **<​COLUMN_NAME>​_evidence_values** - This is easy to read common reference ​values for this column ​in "|" separated ​format for multiple entriesThese are usually terms that classify or annotate a gene. ExamplesGroup ClassificationsOntology Terms etcThis column ​will contain ​"​-" ​if not applicable. +  - **<​COLUMN_NAME>​_evidence_values** - This column contains human readable ​values ​used as evidence ​for corresponding values in the <​COLUMN_NAME>​_values column. For example, if <​COLUMN_NAME>​_values contains a Gene Ontology Term, this column ​might contain a reference to a publication where that mapping was first indicated. If there is multiple evidence values for one <​COLUMN_NAME>​_values entry, they will be separated by "," ​with unique sets being separated ​by "​|"​For example, if <​COLUMN_NAME>​_values contains there term "​nucleus|cell wall" this column may containCostessi A (2011),Wee S (2002)|Okumura F (2012) indicating that COSTESSI A and WEE S both refer to nucleus, and OKUMURA refers to cell wallIf no evidence values are provided, this will be "​-"​ 
-  - **<​COLUMN_NAME>​_evidence_ids** - These are ids that correspond to the values in <​COLUMN_NAME>​_values. For example, if <​COLUMN_NAME>​_values contained the gene ontology term: nucleus, this column ​may contain ​the corresponding ​GO ID of GO:0005634This column ​will contain ​"​-" ​if not applicable. +  - **<​COLUMN_NAME>​_evidence_ids** - These are ids that correspond to the values in <​COLUMN_NAME>​_evidence_values. For example, if <​COLUMN_NAME>​_evidence_values contains Costessi A (2011),Wee S (2002)|Okumura F (2012), this column ​might contain: 138657,​58230|140283 ​corresponding ​to BioGRID publication IDsIf no evidence ids are provided, this will be "​-"​ 
-  - **<​COLUMN_NAME>​_evidence_classes** -  +  - **<​COLUMN_NAME>​_evidence_classes** - This column contains the class of evidence being presented. It contains generic terms representing sources of evidence such as PUBLICATION|INTERPRO|PFAM. If no evidence classes are provided, this will be "​-"​ 
-  - **<​COLUMN_NAME>​_evidence_methods** - +  - **<​COLUMN_NAME>​_evidence_methods** - This column contains whether or not the evidence is considered to be experimentally derived or inferred. Each piece of evidence can have an associated method. If no evidence methods are provided, this will be "​-"​.
  
  
 
biogrid_projectindex.txt · Last modified: 2018/09/13 01:47 by biogridadmin