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WP4 Current status

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WP4 Current status

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  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. WP4Current status Paolo Romano & WP4 group EBRCN General Meeting, Genova, 26-28/03/2003

  2. WP4: Linking to Medline (i) Retrieval of PUBMED IDs still ongoing • MK amending DSMZ literature db (40% - 60%) • FG supporting BCCM, manual insertion after restructuring of dbs • GS retrieving PMIDs for CBS catalogues • PR retrieving PMIDs for NCCB catalogues • Approaching CIP, CABI, NCIMB • ECACC? EBRCN General Meeting, Genova, 26-28/03/2003

  3. WP4: Linking to Medline (ii) Catalogue structures • ongoing (collections’ tasks) • done for ICLC, BCCM/LMBP, DSMZ (maybe other as well) SRS structure and syntax files • ongoing, based on Catalogue Production guidellines • completed during conversion to SRS 7 • done for ICLC and BCCM/LMBP EBRCN General Meeting, Genova, 26-28/03/2003

  4. WP4: Linking to Medline (iii) Catalogues updated:  ICLC: November 2002  BCCM/LMBP: March 2003 • DSMZ Literature db: May 2003 (plan) • Other BCCM, NCCB plasmids: at next catalogue update EBRCN General Meeting, Genova, 26-28/03/2003

  5. WP4: Linking to other Literature Some literature refs are missing from Medline • Biosis & Embase available for downloading by BD • CABI abstracts • check how many recent literature refs are not in Medline, and are either in Biosis or Embase or CABI Abstracts EBRCN General Meeting, Genova, 26-28/03/2003

  6. Linking to EMBL (i) • Test for linking to EMBL Data Library through SRS, without IDs, gave negative results: • Links are different for different materials and can use various EMBL fields: • Organism (micro-organisms), Division (viruses and plasmids), Feature Table (definition of the source through Key, Qualifier, Description) • Annotation problems (e.g., missing spaces) • Indexing problems (e.g., use of dots) EBRCN General Meeting, Genova, 26-28/03/2003

  7. Linking to EMBL (ii) Examples of search: • Query: Fungi & 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, Genova, 26-28/03/2003

  8. Linking to EMBL (iii) • Identify ID based crossreferences for linking from CABRI catalogues to EMBL (and viceversa) • A huge number of EMBL records could be linked to a single CABRI item • Add links in EMBL and use these links when linking from CABRI (search by SRS) • ID based links to CABRI included in EMBL data library and distributed with it EBRCN General Meeting, Genova, 26-28/03/2003

  9. Linking to EMBL (iv) • Agreement with EBI (list of crosserefs) • Work do be done after uploading to EBI of CABRI extracted catalogues: end of june 2003 • Table of crossreference returned to collections • Possible well known “wrong” EMBL sequence removed from table • Links from plasmids catalogues to EMBL managed differently (using current remarks) EBRCN General Meeting, Genova, 26-28/03/2003

  10. Linking to other sources • Links to maps of BCCM/LMBP plasmids added in a new field: next catalogue update • Images of micro-organisms (CBS & BCCM) added in a new field: starting from next updates • Further links (nomenclature, acronyms, genes) under analysis • D10: integrated Biological Resource database • Interconnected vs integrated EBRCN General Meeting, Genova, 26-28/03/2003

  11. Extracted databases Extracted databases • Selected meaningful subset of information: MDS+link to main CABRI site • Established agreement with EBI • Preparation of catalogues, using SRS: end of April 2003 • Setting up of a purpose FTP site: end of April 2003 • Upload of catalogues to EBI: end of May 2003 • Automatic updating by EBI by FTP through SRS Prisma EBRCN General Meeting, Genova, 26-28/03/2003

  12. Inventory of data usage and sets M12: ”Inventory of BRC data usage and data sets completed to enable the identification of data sources needed to provide a comprehensive information centre on BRCs and their holdings” • Methodologies and Protocols • Reference lists (acronyms, countries, bacterial nomenclature) • Internal papers/thesis • CABRI guidelines EBRCN General Meeting, Genova, 26-28/03/2003

  13. Inventory of data usage and sets • List of data sets, by category, with links to infomration sources • Searchable database with links to information sources • GlobalSearch applied to partners’ web site • ht://Dig can be used to index all partners’ site and search their contents in a unique step (only static files, not searchable archives/databasess) EBRCN General Meeting, Genova, 26-28/03/2003

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