BioGRID PROJECTINDEX Formatted Downloads
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| [[downloads|Back to BioGRID Download Formats]] | [[downloads|Back to BioGRID Download Formats]] | ||
| - | ==== How to Detect a BioGRID CHEMTAB file ==== | + | ==== How to Detect a BioGRID PROJECTINDEX file ==== |
| - | BioGRID CHEMTAB files are denoted by the extension **.chemtab.txt** or **.chemtab.zip** | + | BioGRID PROJECTINDEX files are denoted by the extension **.projectindex.txt** or **.projectindex.zip** |
| ==== Header Definitions ==== | ==== Header Definitions ==== | ||
| - | The first line of a BioGRID CHEMTAB file is the heading line and starts with a hash (#). This line is purely for informational purposes and gives a brief description of the content contained in each column. If you are scripting the use of this file, you can simply ignore it. | + | The first line of a BioGRID PROJECTINDEX file is the heading line and starts with a hash (#). This line is purely for informational purposes and gives a brief description of the content contained in each column. If you are scripting the use of this file, you can simply ignore it. |
| ==== Column Definitions ==== | ==== Column Definitions ==== | ||
| - | The column contents of BioGRID CHEMTAB files should be as follows: | + | The column contents of BioGRID PROJECTINDEX files will always contain the following columns: |
| + | |||
| + | - **BioGRID ID** is the identifier in the BioGRID database that corresponds to the gene. These identifiers are best used for creating links to the BioGRID from your own websites or applications. To link to a page within our site, simply append the URL: http://www.thebiogrid.org/ID/ to each ID. For example, http://www.thebiogrid.org/31623/. | ||
| + | - **Entrez Gene ID** is the identifier from the Entrez-Gene database that corresponds to the interacting gene. If no Entrez Gene ID is available, this will be a "-". | ||
| + | - **Systematic name** is a plain text systematic name if known for the gene. Will be a "-" if no name is available. | ||
| + | - **Official symbol** is a common gene name/official symbol for the gene. Will be a "-" if no name is available. | ||
| + | - **Synonyms/Aliases** is a "|" separated list of alternate identifiers for the gene. Will be "-" if no aliases are available. | ||
| + | - **Organism ID** is the NCBI taxonomy ID for the gene. | ||
| + | - **Organism Name** is the official name of the organism for the gene. | ||
| + | - **Interaction Count** is the number of interactions in the BioGRID for this gene. | ||
| + | - **PTM Count** is the number if post translational modifications in the BioGRID for this gene. | ||
| + | - **Chemical Interaction Count** is the number of chemical interactions in the BioGRID for this gene. | ||
| + | - **Source** is the source database for the curation of this gene within this project. | ||
| + | |||
| + | === 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: | ||
| + | |||
| + | - **<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>_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 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 contain: Costessi A (2011),Wee S (2002)|Okumura F (2012) indicating that COSTESSI A and WEE S both refer to nucleus, and OKUMURA refers to cell wall. If no evidence values are provided, this will be "-" | ||
| + | - **<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 IDs. If no evidence ids are provided, this will be "-" | ||
| + | - **<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** - 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 Chemical Interaction ID**. A unique identifier for each interaction within the BioGRID database. | ||
| - | - **BioGRID ID** for Gene Interactor. The identifier in the BioGRID database that corresponds to the interacting gene. These identifiers are best used for creating links to the BioGRID from your own websites or applications. To link to a page within our site, simply append the URL: http://www.thebiogrid.org/ID/ to each ID. For example, http://www.thebiogrid.org/31623/. | ||
| - | - **Entrez Gene ID** for Gene Interactor. The identifier from the Entrez-Gene database that corresponds to the interacting gene. If no Entrez Gene ID is available, this will be a "-". | ||
| - | - **Systematic name** for Gene Interactor. A plain text systematic name if known for the interacting gene. Will be a "-" if no name is available. | ||
| - | - **Official symbol** for Gene Interactor. A common gene name/official symbol for the interacting gene. Will be a "-" if no name is available. | ||
| - | - **Synonyms/Aliases** for Gene Interactor. A "|" separated list of alternate identifiers for the interacting gene. Will be "-" if no aliases are available. | ||
| - | - **Organism ID** for Gene Interactor. An NCBI taxonomy ID for the interacting gene. | ||
| - | - **Organism Name** for Gene Interactor. The official name of the organism for the interacting gene. | ||
| - | - **Action**. Chemical action for this interaction. | ||
| - | - **Interaction Type**. Methods such as target, enzyme, carrier, transporter, etc. | ||
| - | - **First author surname** of the publication in which the interaction has been shown, optionally followed by additional indicators, e.g. Stephenson A (2005) | ||
| - | - **Pubmed ID** of the publication in which the interaction has been shown. | ||
| - | - **BioGRID Publication ID**. This is the internal BioGRID reference id for this publication. Useful for linking to BioGRID publication pages, such as: http://thebiogrid.org/101382/publication/ | ||
| - | - **BioGRID Chemical ID**. The internal BioGRID identifier for the interacting chemical. | ||
| - | - **Chemical Name**. Common name for the Chemical. | ||
| - | - **Chemical Synonyms**. A "|" separated list of synonyms for this chemical. Will be "-" if non-exist. | ||
| - | - **Chemical Brands**. A "|" separated list of brand names for this chemical. Will be "-" if non-exist. | ||
| - | - **Molecular Formula**. A molecular formula for this chemical, will be "-" if unknown. | ||
| - | - **Chemical Type**. Will be "-" if unknown. | ||
| - | - **Chemical ATC Codes**. A "|" separated list of ATC codes for the chemical. Will be "-" if unknown. | ||
| - | - **Chemical CAS Number**. Will be "-" if unknown. | ||
| - | - **Curated By**. Name of the database interaction was curated by. | ||
| **All columns are mandatory so columns with no values are filled with "-"** | **All columns are mandatory so columns with no values are filled with "-"** | ||
| [[downloads|Back to BioGRID Download Formats]] | [[downloads|Back to BioGRID Download Formats]] | ||