What's New at RGD
This page is a listing of significant changes at the Rat Genome Database.
- GENES FTP file Format Changing–Effective immediately we are generating new Gene extract files for RGD within our FTP site. There are three new files: GENE_RAT, GENES_HUMAN, and GENES_MOUSE which contain all the Genes the RGD database knows about.
The existing GENES file will no longer be updated and will be removed in no less than 2 months from now.
This change was necessary due to inconsistencies we found within this file while trying to parse it ourselves. Also we are now handling genes from all species in a consistent manner within our own database. Please see this RCF posting for a full description of the file changes. These files will be updated every week going forward.
- Nearly 17,000 Genes with Gene Ontology Annotations! – Increased manual curation efforts and automated pipelines have allowed RGD to increase the number of genes with functional information to 16,959. There are over 136,273 GO annotations in RGD as well as nearly 8,000 phenotype, disease and pathway annotations.
- GOA Annotations from EBI – RGD has implemented a new pipeline to add GO annotations from GOA at EBI to RGD genes. The initial download added more than 60,000 annotations. Downloads will occur monthly to keep RGD current with GOA releases
- Weekly Data Releases – All data added obtained through manual curation and data pipelines each week is released on Saturday to ensure the most up to date information is available to users in a timely manner.
- New FTP Files Weekly – FTP files are also updated on a weekly basis.
- EntrezGene Synchronization – A major update of genes from EntrezGene in November added more than 15,000 new genes and pseudogenes to RGD. Weekly updates from EntrezGene continue to add new genes as well as new identifiers for Genbank, Unigene, Uniprot, KEGG, PubMed.
- Increased Biological Annotations – Improvements in curation software and processes make it possible for RGD to add approximately 500 biological annotations weekly for genes, QTL and strains. Annotations include those for the Gene Ontology (function, biological process, cellular component); Mammalian Phenotype, Disease (utilizing MeSH terms) and Pathways (using RGD’s Pathway Ontology).
- New Disease Portals – The new Cardiovascular Disease Portal and new version of the Neurological Disease Portal create easy access to a variety of data for the disease researcher.
- Sequence Annotation – The Genome Conflict Submission Form and the Genome Repair Kit on GBrowse illustrate RGD’s continued commitment to the community to provide sequence annotation services.
RECENT DEVELOPMENTS THAT WILL MAKE 2007 A STELLAR YEAR FOR RGD USERS
- The Pied Piper, December 2006 Issue
RGD publishes new issue of The Pied Piper. The December 2006 publication includes articles on a new Cardiovascular Disease Portal, a Genome Repair Kit, NCBI Genome Updates, a new tool at EMBL-EBI, and rat research news. The Pied Piper also contains rat resource links, RGD Facts and Functions, upcoming conferences and updated data statistics and tools available at RGD. Subscribe to future issues of the Pied Piper.
- Announcing the New Cardiovascular Disease Portal
The new Cardiovascular Portal at RGD provides a comprehensive resource that integrates diverse data types and analysis tools. This dynamic portal offers researchers a unique opportunity to locate related cardiovascular disease information in one centralized location. The Cardiovascular Disease Portal homepage offers users a summary of data within the portal and several options to view and access data. The portal homepage invites users to customize a results page by allowing users narrow results by specific disease or disease category. Once a specific disease is chosen, the disease portal will provide a list of related genes, QTL, and strains along with a genomic view of these objects as well as access to related Genome Browser results. The portal also offers sections for Phenotypes, Biological Processes and Pathways related to cardiovascular disease. We invite you to visit the new Cardiovascular Disease Portal at RGD and take advantage of the excellent resource for cardiovascular disease information.
- A Genome Repair kit is now available on RGD
RGD’s Genome Browser (GBrowser) has a new addition, conflict tracks. In order to alert users to potential problem areas, we have mapped the positions of 6 regions, covering 250 Kb to 6Mb each, that differ in chromosomal assignment between the Baylor 3.4 and Celera assemblies. Additional conflicts will continue to be added as they are found.
Have you identified regions of conflict or other sequence errors? Let us know! RGD has a simple form you can use to report conflicts. We will contact you for details, add the data to GBrowse, and forward these conflicts to the appropriate place, such as Baylor or RGD curation staff, for resolution. Please Contact RGD with any questions.
- RGD adds link to Physgen
The Rat Genome Database (RGD) website will now include a link to Physgen. The PhysGen logo appears on the upper portion of RGD pages and links directly to the PhysGen homepage.
- Try the New Version of the Neurological Disease Portal!
RGD will be launching a new version of the Neurological Disease Portal. Please try the beta version and give us your feedback. Send your suggestions to Mary Shimoyama at mshimoyama@hmgc.mcw.edu. We look forward to your input.
- New Form to Report Genome Sequence Conflicts
We have created a Genome Conflict Submission Form that will allow users to report any conflicts they find in the genome sequence or annotations. The form is accessible from the navigation bar at the top of every page as well as on the Genome Browser. On this simple form you can indicate what regions are in question; we will then contact you for the details. These regions will be reported to Baylor to use as they continue to improve the assembly. In addition we will shortly be adding a track on the Rat Genome Browser that will indicate these regions.
- The Pied Piper, June 2006 Issue
RGD publishes new issue of The Pied Piper. The June 2006 publication includes articles on a new tool for rat research, upcoming conferences, resources at Entrez, and research information. The Pied Piper also contains rat resource links and updated data statistics and tools available at RGD. Subscribe to future issues of the Pied Piper.
- PhysGen Announces the Availability of Mutant Rats
PhysGen, one of five Programs for Genomic Applications (PGA) funded by the National Heart, Lung and Blood Institute is currently generating knockout rats using an ENU (N-ethyl-N-nitrosourea) mutagenesis strategy. Male rats were subjected to ENU and bred to healthy female rats to generate F1 heterozygous offspring. Prior to phenotypic screening, the offspring are screened by TILLING, a high-throughput method which identifies mutations by enzyme cleavage of heteroduplex PCR product formation between wild-type and mutated alleles. During the screening process, several amino acid changes were identified in targeted genes. Confirmed gene knockouts will be phenotypically characterized and data will be released on the PhysGen website. We are pleased to make the rats with amino acid changes available to interested investigators (click for details). Heterozygous mutant rats (5M/5F) will be available on a first come-first serve basis for 75 days after posting on PhysGen’s website. For additional information on how to obtain these rats, please contact Melinda Dwinell at (414) 456-4498.
- Announcing the Neurological Disease Portal
RGD has released its Neurological Disease Portal to provide researchers with easy access to data on genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource, partially funded by NINDS also includes dynamic data analysis tools to make it a one stop resource for neuroscience researchers. The user chooses a disease category to get a pull-down list of diseases. A single click on a disease will provide a list of related genes, QTLs, and strains as well as a genome wide view of these across the genome via GViewer and access to GBrowse results showing the genes and QTLs within the genomic context. Additional pages for Biological Processes, Pathways and Phenotypes provide one-click access to data of interest. A Tools section and a Links section provide additional resources. To suggest additional data or tools for incorporation into the portal, please contact Mary Shimoyama. A Cardiovascular Disease Portal is scheduled for release in Spring 2006. Watch for it!
- RGD publishes in Physiological Genomics
An RGD article entitled "Tools and Strategies for Physiological Genomics - the Rat Genome Database" was published in the October 2005 issue of Physiological Genomics. The article describes the various tools available at RGD and outlines strategies for their use in a number of common research 'tracks' including Positional Cloning, Comparative Genomics, Expression Profiling and Functional Genomics. The article (full text and PDF) is freely available: Read Article.
- The RGD staff wishes to announce its continued service to the scientific community. The NHLBI has recently granted continued support of RGD for another 4 years
We would like to express our thanks to the many groups that make RGD possible:- Researchers, who accessed RGD over 3.4 million times last year
- NHLBI for their support and guidance through the years
- Supporters in the research community, who submitted letters of support
- RGD Strategic Advisory Board for their support and guidance
- New edition of The Pied Piper
RGD publishes new edition of The Pied Piper. The June 2005 publication includes articles on The Mammalian Gene Collection (MGC), The National Bio Resource Project in Japan (NBRP), New Disease Portals at RGD, NCBI’s Entrez Genome Project and Pied Piper Proposal Submission. The Pied Piper newsletter also contains upcoming conferences, rat resource links and updated data statistics and tools available at RGD. Subscribe to future issues of the Piped Piper.
June 10, 2005:
- RGD at the ISMB 2005 conference
RGD will be hosting 2 presentations at the ISMB 2005 conference in Detroit, Michigan.- Rat Genome Database: A Database for Comparative Genomics using the Rat Model Organism
June 28, 2005 2-3 PM in Nicolet Room. more details ... - Multiple Ontologies in RGD June 24, 2005. more details ...
- Rat Genome Database: A Database for Comparative Genomics using the Rat Model Organism
- RGD at the PLoS Computational Biology Poster Session
RGD will present 3 posters at the PLoS Computational Biology Poster Session June 28, 2005.
- VCMap - Virtual Comparative Map Tool
- GViewer - Genome Viewer Tool for rat and human
- Implementing complex phenotype data into RGD
We hope to see you at the presentations and poster sessions!
- GBrowse Updates
- New track selection interface added to enhance the selection of tracks based on environmental factors, strains used, and organs tested
- New Disease Portals
RGD has released a prototype for its Disease Portal project. To better serve the diverse research communities interested in rat, human and mouse data related to disease, RGD is developing disease portals to direct users to the data of most interest to them. The current prototype is the first stage in a comprehensive project of data collection, annotation and data mining software development that RGD is implementing to aid researchers in their pursuit of the
mechanisms of disease. We are interested in feedback regarding the format of the portals, as well as data and tools our users would like to see become part of these portals.
Some RGD Disease Data Figures:- Number of Diseases represented in RGD: 502
- Number of Disease Annotations: 2643
- Number of Disease Annotations for Rat Genes: 1004
- Number of Disease Annotations for Rat QTLs: 934
- Number of Disease Annotations for Rat Strains: 171
RGD error track on GBrowse
RGD has developed a prototype GBrowse track that will show regions of the current assembly that have identified errors. Where the repair is known, this is also displayed. Clicking on any bactig within this region will take you to an error report. Try it and let us know what you think.
- New micro-array portal added to RGD
RGD has created a portal to enable users to access tools and data related to microarray and expression data. Click to Try it!.
- Beta version released of a new virtual comparative map, based on gene physical map positions
The new sequence based virtual comparative map was added to the VCMap tool.
Syntenic regions are determined through NCBI's homologene data
and UCSC genomic data.
Advantages of the new map include:- Marker locations are based on genomic coordinates
- Syntenic regions are calculated based on NCBI homologene data
- Validity is increased by using recipricol best hits
- Validity is increased by using only experimentally validated genes
- RGD recently updates:
- 7501 predicted genes with a high confidence level loaded into RGD
- RGD now has a new strain FTP file
- New Browser section added to the Genes report. Section adds hyperlinks to the corresponding genomic region in various tools: UCSC, NCBI, Ensembl, ECR, Vista, and GBrowse
- RGD was recently published in Nucleic Acids Research
The RGD was published in Nucleic Acids Research with a title of "The Rat Genome Database (RGD): developments towards a phenome database". Click to see this article.
- RGD Adds Scoreboard
The homepage of RGD now shows running totals of data in the database. These totals include the number of genes, QTL, strains, and biological annotations. The scoreboard is at the bottom right corner of the homepage.
- RGD hosted a free demo and a booth
at the Society for Neuroscience Meeting
Free RGD Demo/satellite event will be at the San Diego Marriot Hotel and Marina
October 22, 2004 9 AM - 12 PM Del Mar room
We will demonstrate the functionality of RGD, including:
* how to navigate the database to find the information you desire
* how to use the many tools avaliable
* how to submit your own data for inclusion in RGD.
Please let us know if you are interested in attending by sending us an email at curation@rgd.mcw.edu
A limited number of laptops will be at the demo, so please bring your own laptop with wireless capability for the hands-on training.
RGD will be at booth 804
October 24 to 27, 2004 9:30 AM to 5 PM
September 20, 2004:
- RGD has released a new genome viewing tool called Gviewer
The Gviewer gives a genome view on a RGD ontology
report page of records that match a query statement.
* Zoom in or out by right clicking the image
* View a single chromosome by clicking on one
* Symbols are hyperlinked to RGD reports
* Bars are hyperlinked to the region in the RGD genome browser
* View and save all displayed records in an excel file
View the tool's results by using the following terms in the ontology browser:
Increased Blood Pressure
Diabetes Mellitus, Non-Insulin-Dependent
Alzheimer's Disease
Parkinson's Disease
- RGD Adds Biological and Variation Tracks to GBrowse
RGD has added 24 new tracks to GBrowse to attach biology to the genome and provide a view of variation across the genome.
New Tracks include:- 22 New Ontology tracks based on annotations from Gene Ontology, Mammalian Phenotype Ontology, Disease Ontology and our Pathway Ontology
- 3 Types of Ontology Tracks:
- All Terms Track - Shows the sequence feature and all terms annotated to it
- Best Evidence Track - shows individual sequence features annotated at least once to an ontology term. The track color reflects the highest evidence code for the assignment.
- Parent Term Track - This track groups together sequence features annotated to a higher term (from the second level of the graph) or its descendants.
- SNP track - SNPs from dbSNP are displayed
- A SNP Density overview - Shows the number of SNPs per MB
Some of the new functions these tracks allow include:
- Announcing the new version of the GATool
RGD has released a new version of the Gene Annotation Tool which allows the user to mine RGD, Entrez Gene, UniProt (SwissProt) and KEGG for functional information on gene sets.
New improvements include:
* Very significant increase in speed
* Genomic position input using basepairs or markers
* New ID types for input:
Affy IDs, GenBank IDs (including ESTs), LocusLink IDs, UniProt (SwissProt), KEGG IDs
* Ability to accept files of thousands of identifiers
* Options to retrieve RGD phenotype and disease ontology terms as well as GO terms
* Color coded results based on databases
Try it!
- Announcing Pathway Annotations at RGD
The first release of RGD’s pathway annotation project includes 373 annotations for 12 pathways. In an effort to add and integrate data from metabolic, signaling, regulatory and disease pathways, RGD has developed a controlled vocabulary based on the concepts of other biological vocabularies such as Gene Ontology (Gene Ontology Consortium) and the Mammalian Phenotype Ontology (MGD and RGD). This annotation methodology was developed to allow RGD to integrate data from major pathway databases such as KEGG and Reactome. Search pathway data using the ontology browser using a term such as “cell death” and highlight “pathway ontology”. Click here to see a pathway report. Watch for additional annotations and pathways as well as links to pathway maps in the coming months.
- The new RGD QTL pages have many new features
* Introductory page has options for selecting species (rat, mouse, human, or all)
* Query page has three new options to search for QTL based on the QTL's reference paper
1. Keywords in the reference paper's title or citation
2. Author Surname
3. Year of publication
* Result page has genomic coordinates, if they are known
* Result page has hyperlinks to UCSC and/or RGD Genome Browsers
* Report page has LOD plot graphics capabilities, if graphic data was submitted to RGD
Try the new query form, or see an example of the new graphics capability on a report.
ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non-conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project.
Try it!
- RGD Updated VCMap tool
112 Human QTLs added, 1700 Mouse QTLs added, and 540 Rat QTLs added. Human and Rat QTL maps have either SSLP or Gene markers. Try it!
- RGD will be at the XVth International Workshop on Genetic Systems in the Rat 2004
Copenhagen, Denmark on 9th-12th Sept 2004 to be held at the Scandic Copenhagen Hotel.
View the meeting's website here.
- New manually curated Annotations added:
* 1,819 new disease and phenotype annotations to genes, strains, QTL
* 659 new gene ontology annotations
* 1,800 rat, human, and mouse QTLs added
July 1, 2004:
- RGD released a new tool: Genome Annotation
Tool
Users can enter a query using either genomic coordinates or Genbank IDs. The tool reports all known mRNAs, ESTs, Unigenes, homologs that exist between those genomic coordinates. Try it!
- RGD data displayed on UCSC browser
RGD genes, SSLPs, and QTLs are now displayed on the UCSC browser. Try it!
- RGD now has links to KEGG
The gene reports now link to KEGG reports. User can then access all of the pathway data from the KEGG reports. See new KEGG link.
- RGD has released new SSLP query and report pages
- RGD has released an updated version of the QTL query and report pages
- Added query capability for human QTLs
- New hyperlinks to Vista tools from the Browsers section on the report
page
Try it!
-
New features include:
• Query Page:
Query by map location range on various maps
Query for SSLPs with allele data
• Results Page:
Download query results into Excel format
Download all available map data for selected markers and all results
Popup window to display the multiple maps and chromosomes a marker is on
• Report Page:
New browser section with hyperlinks to UCSC, VCMap, ECR, Vista, etc.
New Strain Variations report
New RGD reference format
New external database format
Try it!
- New RGD Data Updated:
- 321,348 Sequences added
- 2,493 Gene Ontology annotations
- 1,088 Disease Ontology annotations
- 629 Phenotype Ontology annotations
- 253 Refrences added
- 234 SSLPs added
- 196 QTLs added
- 124 Strains added
- 17 Genes added
- 3 Homologs added
- International Human Full-Length cDNA Annotation Effort Validates 21,037 Genes:
Providing a major advance in the efforts to elucidate the functional units of the human genome, an international consortium led by Takashi Gojobori of the Institute of Advanced Industrial Science and Technology in Japan has validated 21,037 genes and identified 5,155 new gene candidates through a combination of computer algorithms and expert human analysis of 41,118 full-length cDNAs. Results of this project are available in the H-Invitational Database. This massive undertaking involved over 150 scientists from 12 countries. At the invitation of the Japanese organizing group and through its sponsorship and that of the DOE, RGD contributed the largest number of American participants. RGD staff was involved in the organization and implementation of the annotation efforts, and along with Swiss-Prot developed the protocols and manual used in the annotation of the full-length cDNAs. Two major annotation marathons were held in which RGD staff contributed more than 10% of the total annotations completed. The H-Invitational Database will be an invaluable resource for researchers developing a complete functional description of the human genome and was a result of the type of international cooperation and large-scale collaboration that produced the human genome sequence three years ago.
- Some RGD tools updated or improved:
- Updated RH Map Server
Has options to select different framework maps
Place your markers on the RH map 2.0 or 3.0 framework maps
Try it!
- Improved quick search accessed from the query box on the header of
every page.
Searches for matches in controlled vocabulary terms, synomyms, and descendants
Searches the curator annotations on RGD objects
Searches using wildcards
Allows for batch downloading of results
Try it! ( click on GO button at right-top of every page)
- New Advanced Search accessed from the hyperlink on the header
of every page
Searches using booleans (AND, OR, NOT)
Searches for matches in controlled vocabulary terms, synomyms, and descendants
Searches for curator annotations on RGD objects
Allows for batch downloading of results
Try it!
- Improved QTL search accessed from the Data category in the header
of every page
Searches for matches in controlled vocabulary terms, synomyms, and descendants
Searches for curator annotations on RGD objects
Searches based on genomic locations
New genomic section with hyperlinks to other genomic resources in the same region
Allows for batch downloading of results
Try it!
- New homologs search accessed from the Data category in the header
of every page
Find comparative biological data to rat genes
Try it!
- Updated RH Map Server
- Gene Annotation Tool Updated:
The Gene Annotation Tool was updated to provide visitors with added functionalities and increase the software's robustness. The tool now retrieves data from the RGD database. The tool also has an option to return the query results in HTML format. Under this option, many of the fields are returned as links to report pages in their respective databases. This enables the user to obtain more in depth information from the original source. Try it now.
- New data loaded:
- Almost 2400 new human and mouse homologs of rat genes added
- Data added to over 6000 homologs
- Over 200 new genes added
- Almost 1000 descriptions added to rat genes
- Over 700 manually curated annotations added to rat genes
- 916 Gene Ontology (GO) annotations for 508 genes added
- 17 new strains and 3 new QTLs added
- Watch for the RGD booth at the upcoming Toxicology meeting
RGD
will have a booth (Booth #2117) at the Society
of Toxicology 43rd Annual Meeting, Baltimore, March 21-25, 2004.
The Society of Toxicology (SOT) Annual Meeting is the largest toxicology meeting and exhibition in the world, attracting approximately 6,000 scientists from industry, academia, and government. The program includes a plenary and other special lectures, symposia, workshops, roundtable discussions, and platform and poster presentations. more...
- New Nomenclature Guidelines added:
Nomenclature Guidelines for genes, alleles, QTL, and other loci have been approved by the Rat Genome and Nomenclature Committee and are now available on RGD.
- New data loaded:
• Over 3,200 rat homologs added
• Over 1,800 manually curated annotations added to genes
• Over 460 rat gene descriptions added
• 13 new strains added
- RGD will link to MCW's mirror site for the
UCSC Genome Browser:
RGD will link to The Medical College of Wisconsin's mirror site for the University of California - Santa Cruz (UCSC) Genome Browser.
View now.
RGD Milestones (2000 - 2003)
