WP4 Current status

1
WP4Current status

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• Paolo Romano WP4 group

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?

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

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

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

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)

7
Linking to EMBL (ii)

• Examples of search
• Query Fungi source cbs 100.20( (
  (emblrelease-FtKeysource
  emblrelease-FtQualifierstrain ( (
  emblrelease-FtDescriptioncbs
  emblrelease-FtDescription100 )
  emblrelease-FtDescriptioncbs100 )
  emblrelease-FtDescription20) ) lt
  emblrelease-Organismfungi )

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

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)

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

11
Extracted databases

• Extracted databases
• Selected meaningful subset of information
  MDSlink 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

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

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)