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EBRCN General Meeting, Paris, 28-29/11/20021 WP4 Analysis of non-EBRCN databases and network services of interest to BRCs Current status Paolo Romano Questa.

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Presentazione sul tema: "EBRCN General Meeting, Paris, 28-29/11/20021 WP4 Analysis of non-EBRCN databases and network services of interest to BRCs Current status Paolo Romano Questa."— Transcript della presentazione:

1 EBRCN General Meeting, Paris, 28-29/11/20021 WP4 Analysis of non-EBRCN databases and network services of interest to BRCs Current status Paolo Romano 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.

2 EBRCN General Meeting, Paris, 28-29/11/ 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

3 EBRCN General Meeting, Paris, 28-29/11/ 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

4 EBRCN General Meeting, Paris, 28-29/11/ 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)

5 EBRCN General Meeting, Paris, 28-29/11/ 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

6 EBRCN General Meeting, Paris, 28-29/11/ 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

7 EBRCN General Meeting, Paris, 28-29/11/ 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

8 EBRCN General Meeting, Paris, 28-29/11/ 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

9 EBRCN General Meeting, Paris, 28-29/11/ 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)

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

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

12 EBRCN General Meeting, Paris, 28-29/11/ 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*] )

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

14 EBRCN General Meeting, Paris, 28-29/11/ 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


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