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--- biogrid_ptmtab_ptmrel [2015/04/25 04:27]
biogridadmin [Column Definitions]
+++ biogrid_ptmtab_ptmrel [2017/08/08 12:52]
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-====== BioGRID PTMTAB,PTMREL Format Downloads ======
-The BioGRID PTMTAB and PTMREL formats are custom BioGRID formats that are designed to provide the entirety of our post translational modification curation efforts in a format that is simple to read in Microsoft Excel or to script into Bioinformatics applications. All Columns are separated by tabulations.
-[[downloads|Back to BioGRID Download Formats]]
-===== PTMTAB File Details =====
-==== How to Detect a BioGRID PTMTAB file ====
-BioGRID PTMTAB files are denoted by the extension **.ptmtab.txt** or **.ptmtab.zip**
-==== Header Definitions ====
-The first line of a BioGRID PTMTAB 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 ====
-The column contents of BioGRID PTMTAB files should be as follows:
-  - PTM ID. A unique identifier for each post translational modification within the file. These IDs are non-persistant and only relevant to this specific file download.
-  - Entrez Gene ID. The identifier from the Entrez-Gene database that corresponds to this PTM Site. Will be a ”-” if no entrez gene is available.
-  - BioGRID ID. The identifier in the BioGRID database that corresponds to this PTM Site. 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/.
-  - Systematic name. A plain text systematic name if known. Will be a "-" if no name is available.
-  - Official symbol. A common gene name/official symbol. Will be a "-" if no name is available.
-  - Synonyms/Aliases. A "|" separated list of alternate identifiers. Will be "-" if no aliases are available.
-  - Sequence. A protein sequence referenced for this PTM Site.
-  - Refseq ID. The Refseq ID of the Sequence.
-  - Position. Residue position within the sequence for this PTM Site.
-  - PTM Type. A descriptive name for the type of PTM Site referenced (examples: Phosphorylation, Ubiquitination)
-  - Residue. The residue that is in location in Position within the Sequence.
-  - 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.
-  - Organism ID. This is the NCBI Taxonomy ID for this Sequence.
-  - Organism Name. This is the NCBI Taxonomy Classification for this Sequence.
-  - Has Relationships. Will be TRUE or FALSE. When TRUE, this PTM Site will have accompanying relationships within the PTMREL data file.
-  - Qualifications. If additional plain text information was recorded for an interaction, it will be listed with unique qualifiers separated by "|". If no qualification is available, this field will contain "-".
-  - Source Database. This field will contain the name of the database in which this interaction was provided.
-**All columns are mandatory so columns with no values are filled with "-"**
-===== PTMREL File Details =====
-==== How to Detect a BioGRID PTMREL file ====
-BioGRID PTMREL files are denoted by the extension **.ptmrel.txt** or **.ptmrel.zip**
-==== Header Definitions ====
-The first line of a BioGRID PTMREL 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 ====
-The column contents of BioGRID PTMREL files should be as follows:
-  - PTM ID. An identifier denoting which PTM ID (in the PTMTAB file) this relationship is in reference to. These IDs may be repeated if multiple relationships are recorded.
-  - BioGRID ID. The identifier in the BioGRID database that corresponds to this relationship reference. 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. The identifier from the Entrez-Gene database that corresponds to this relationship reference. Will be a ”-” if no name is available.
-  - Systematic name. A plain text systematic name if known. Will be a "-" if no name is available.
-  - Official symbol. A common gene name/official symbol. Will be a "-" if no name is available.
-  - Synonyms/Aliases. A "|" separated list of alternate identifiers. Will be "-" if no aliases are available.
-  - Relationship. A plain text descriptor of the type of relation represented.
-  - Identity. A plain text descriptor of additional identity details if available.
-  - 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.
-  - Organism ID. This is the NCBI Taxonomy ID for this relationship reference.
-  - Organism Name. This is the NCBI Taxonomy Name for this relationship reference.
-  - Source Database. This field will contain the name of the database in which this interaction was provided.
-**All columns are mandatory so columns with no values are filled with "-"**
-[[downloads|Back to BioGRID Download Formats]]