318a5c110a86569bd4e4b8fd7263c684245e6049 lrnassar Thu Oct 10 10:54:48 2019 -0700 Changing JSON API to REST API and adding new entry to API help page refs #24282 diff --git src/hg/htdocs/goldenPath/gbdDescriptions.html src/hg/htdocs/goldenPath/gbdDescriptions.html index 398e213..de422bf 100755 --- src/hg/htdocs/goldenPath/gbdDescriptions.html +++ src/hg/htdocs/goldenPath/gbdDescriptions.html @@ -1,93 +1,93 @@

This page is no longer maintained.

This page was retired long ago when the table descriptions for the annotation database stopped being updated. To retrieve the schemas for tables underlying the Genome Browser annotation tracks one can use the Table Browser -using the "describe table schema" button or the JSON API.

+using the "describe table schema" button or the REST API.

refFlat example

    Gene Predictions and RefSeq Genes with Gene Names

    A version of genePred that associates the gene name with the gene prediction information. In alternative splicing situations each transcript has a row in this table.

       table refFlat
   "A gene prediction with additional geneName field." 
       (
       string  geneName;           "Name of gene as it appears in Genome Browser." 
       string  name;               "Name of gene" 
       string  chrom;              "Chromosome name" 
       char[1] strand;             "+ or - for strand" 
       uint    txStart;            "Transcription start position" 
       uint    txEnd;              "Transcription end position" 
       uint    cdsStart;           "Coding region start" 
       uint    cdsEnd;             "Coding region end" 
       uint    exonCount;          "Number of exons" 
       uint[exonCount] exonStarts; "Exon start positions" 
       uint[exonCount] exonEnds;   "Exon end positions" 
       )

The text for this entry is deprecated. Please use the below Table Browser method to access this information.

Current method to use Table Browser or API with refFlat example

Table Browser

Here is the current way to retrieve table descriptions with the Table Browser.

  1. Navigate to the Table Browser for the specific assembly you are interested in that has the data you are seeking. For example, if you are working with the hg19 assembly, you would make that selection: http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19
  2. Select the table from the appropriate group. Or set the group to "All Tables" and find the table you are interested in finding the description of, in this case the refFlat table: http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=allTables&hgta_track=hg19&hgta_table=refFlat
  3. Click the "describe table schema" button and find the table description along with example data displayed and the related Track Description if available.

For more information on using the Table Browser, see the Table Browser User's Guide.

API

Here is the current way to retrieve table descriptions with the API.

You can also access table schema information in JSON notation using our API with a query such as the following:

http://api.genome.ucsc.edu/list/schema?genome=hg38;track=refFlat

Please note the response will be in JSON notation and may need parsing to interpret.

There are also links to our source code in src/hg/lib to discover the autoSql files (.as) that define our tables. Here is an example link to the refFlat.as file: http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/refFlat.as