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History Report Updates September 2, 2008
The History Report has been updated to show the disposition of each CCDS identifier in each NCBI build. This information can be used to track identifiers and their status over time. The disposition categories are: | Made public | Indicates the NCBI build when the CCDS identifier was first publicly available | | | | Withdrawn | Indicates when an identifier was withdrawn from CCDS | | | | Retained | Indicates that a CCDS identifier and version were carried over from the prior NCBI build to the next build without a version increment, indicating the annotation remained stable | | | | Updated | Indicates that a CCDS identifier was carried over from the prior NCBI build, and the CCDS version was incremented, indicating an annotation change | | | | Partial match | Indicates that there was only a partial match between the NCBI and Ensembl annotation in this build | | | | Withdrawn, inconsistent annotation: no match | Indicates that no match was found for this CDS between the NCBI and Ensembl annotation | | | |
| | | Under review, withdrawal: no match | Indicates that no match was found for this CDS between the NCBI and Ensembl annotation. However, the CCDS was already under discussion to withdraw, indicating the loss reflects asynchronous annotation updates. | | | | Reinstated | Indicates when a CCDS identifier that was previously a partial match or no match has been reinstated as a full match. The reinstatement may also include a CCDS version change. |
Using CCDS 38 as an example, the history shows that CCDS 38.1 was made public in NCBI build 35.1, was retained in build 36.2, and was updated to CCDS 38.2 in build 36.3. For CCDS 714, the history shows that CCDS 714.1 was made public in NCBI build 35.1, was a partial match in build 36.2, and was reinstated as a full match in build 36.3.
CCDS Public Notes Available: July 9, 2008
CCDS Public Notes are now available for CCDS IDs that were recently updated or withdrawn, following consensus agreement from the NCBI, UCSC and WTSI/EBI groups. Public Notes will be added prospectively but will not be added comprehensively for previous changes. The purpose of these notes is to provide an explanation to users as to why a particular CCDS was either updated or withdrawn, and/or to explain representation choices for more complex cases. The Public Notes can be found in the Report, above the Sequence ID table, for a given CCDS ID that recently underwent a change in representation. For example, see CCDS ID 7726.2.
CCDS update released for human: May 1, 2008
The NCBI, Ensembl, and Sanger (Havana) annotation of the human reference genome (NCBI build 36.3) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. Existing CCDS IDs were tracked based on re-identification of matching annotation (both identical and partial matches of CCDS collaboration updates that were asynchronous). CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle. This update includes the addition of 2,151 new CCDS IDs and adds 1,249 Genes into the human CCDS set. Human build 36.3 includes a total of 20,159 CCDS IDs that correspond to 17,052 GeneIDs. See the statistics report for details.
Search by build February 26, 2007
A search in the CCDS database will include only current builds by default. To include data from prior builds in the search, change the search selection from Current Builds to All Builds.
Re-query by sequence ID January 10, 2007
When viewing the sequence IDs for a CCDS, you can re-query the CCDS DB by Nucleotide ID or Protein ID by clicking the red "N" or "P" icon, respectively. These two new icons are in the Links column for each sequence ID shown in the table of sequence IDs for a CCDS.
Search capability enhanced November 8, 2006
A new choice named All has been added to the Search box. This choice is now the default selection instead of Gene Symbol. The All search infers the type of search to be performed based on the search term that is entered, eliminating the need to select a type of search: - If the search term entered is a numeric identifier, or a numeric identifier preceded by "CCDS", then a search by CCDS ID is performed.
- If the search term entered appears to be a nucleotide or protein identifier, then a search by Nucleotide ID or Protein ID is performed, respectively.
- If none of the above is true, then a search by Gene Symbol is performed.
The existing search type selections are still available if you want to perform a specific type of search.
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