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