1 / 14

WP4 Analysis of non-EBRCN databases and network services of interest to BRCs Current status

Questa presentazione può essere utilizzata come traccia per una discussione con gli spettatori, durante la quale potranno essere assegnate delle attività. Per memorizzare le attività durante la presentazione: In visualizzazione Presentazione diapositive fare clic con il pulsante destro del mouse

lisbet
Download Presentation

WP4 Analysis of non-EBRCN databases and network services of interest to BRCs Current status

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Questa presentazione può essere utilizzata come traccia per una discussione con gli spettatori, durante la quale potranno essere assegnate delle attività. Per memorizzare le attività durante la presentazione: • In visualizzazione Presentazione diapositive fare clic con il pulsante destro del mouse • Scegliere Appunti presentazione • Scegliere la scheda Attività • Immettere le attività a mano a mano che vengono assegnate • Per chiudere la finestra, scegliere OK • Questa procedura consente di inserire automaticamente le attività assegnate in una diapositiva che verrà visualizzata alla fine della presentazione. WP4Analysis of non-EBRCN databases and network services of interest to BRCsCurrent status Paolo Romano EBRCN General Meeting, Paris, 28-29/11/2002

  2. WP4: databases of interest Short delay: 1 month ca. · Definition of a list of databases and services that could be of interest to BRCs done · Selection of a subsets of those databases and services done EBRCN General Meeting, Paris, 28-29/11/2002

  3. WP4: identifiers and methods · Selection of information of interest to BRCs within selected databases  ongoing, done for Medline & EMBL · Analysis of identifiers and information and of methods for linking  ongoing,  done for Medline EBRCN General Meeting, Paris, 28-29/11/2002

  4. WP4: Pubmed IDs · CABRI catalogue production guidelines update  ongoing, done for Literature in animal and human cells · Retrieval of needed PUBMED IDs for linking  ongoing, done for ICLC, BCCM/LMBP, NCCB plasmids, support from DSMZ (Kracht) and BCCM (Guissart) EBRCN General Meeting, Paris, 28-29/11/2002

  5. WP4: structure and syntax · Catalogue structures update  ongoing, done for Literature in animal and human cells · SRS structure and syntax files  ongoing, depending on deadlines for submission of catalogues, done for ICLC EBRCN General Meeting, Paris, 28-29/11/2002

  6. WP4: catalogues updates Catalogues updates: done ICLC: November 2002  Plasmids and cell lines: January 2003  “Other catalogues”: February 2003  Bacteria: March 2003  Fungi and Yeasts: May 2003 EBRCN General Meeting, Paris, 28-29/11/2002

  7. WP4: EMBL links • EMBL Data Library is the European database for DNA sequences • It is updated daily and a coordination with NCBI and DDBJ ensures its completeness • It is offered at EBI by means of SRS EBRCN General Meeting, Paris, 28-29/11/2002

  8. WP4: EMBL links • Test have been conducted to identify how to link to EMBL Data Library through SRS, without IDs • Tests performed on: • Bacteria and Archaea • Animal and Human Cell Lines • Fungi and Yeasts • Plasmids • Viruses EBRCN General Meeting, Paris, 28-29/11/2002

  9. WP4: EMBL links variability • Links are different for different materials • Links can use various EMBL fields: • All-text (not very useful) • Organism (for micro-organisms) • Division (useful for viruses and plasmids) • Feature Table data (allow for a correct definition of a source through Key, Qualifier, Description) EBRCN General Meeting, Paris, 28-29/11/2002

  10. WP4: EMBL links variability • Example search: CBS 100.20 in CBS_FIL • Fields and values: • Organism: fungi • Ft-Key: source • Ft-Qualifier: strain • Ft-Description: "cbs 100.20" EBRCN General Meeting, Paris, 28-29/11/2002

  11. WP4: EMBL links variability • Annotation problems: • CBS 100.20 can be annotated as CBS 100.20 or CBS100.20 • CBS 112345 can be annotated as CBS12345 • Indexing problems: • CBS 100.20 is indexed as CBS, 100 and 20 • The dot is not included and is used as a space EBRCN General Meeting, Paris, 28-29/11/2002

  12. WP4: EMBL links variability Examples of searches: • Query: Bacteria & source & cip* ( ([emblrelease-FtKey:source] & [emblrelease-FtQualifier:strain] & [emblrelease-FtDescription:cip*]) < [emblrelease-Organism:bacteria*] ) • Query: Cell line & source & dsm* ( ([emblrelease-FtKey:source] & [emblrelease-FtQualifier:cell_line] & [emblrelease-FtDescription:dsm*]) < [emblrelease-Organism:mammalia*] ) EBRCN General Meeting, Paris, 28-29/11/2002

  13. WP4: EMBL links variability Examples of search: • Query: Bacteria & source & cbs 100.20( ( ([emblrelease-FtKey:source] & [emblrelease-FtQualifier:strain] & ( ( [emblrelease-FtDescription:cbs] & [emblrelease-FtDescription:100] ) | [emblrelease-FtDescription:cbs100] ) & [emblrelease-FtDescription:20]) ) < [emblrelease-Organism:fungi*] ) EBRCN General Meeting, Paris, 28-29/11/2002

  14. WP4: extracted databases Extracted databases • Selection of a meaningful subset of information (strain identification) for each material, including links to external dbs/services  ongoing, proposal sent to collections next month EBRCN General Meeting, Paris, 28-29/11/2002

More Related