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WP4

Current status

Paolo Romano & WP4 group

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WP4 objectives

Improved accessibility and interconnection

• Links to external resources• Literature, Sequence, Special interest databases

• Extracted databases• Available at interested SRS sites

• Inventory of data and usage• Local and remote search, sites’ map

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Links to external resources

LiteratureMedline, Taxon

Special interestMicro-organisms images

Plasmids’ maps

SequencesEMBL Data Library

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Links to Medline

Syntax:add [PMID: <number>] after bibliographic reference

Links in place (> 7000): Plasmids: LMBP (375), NCCB (30)

Cell lines: ICLC (294), DSMZ (905)

Fungi: CBS (454)

Yeasts: CBS (1132)

Phages: NCCB (30)

Literature reference file: DSMZ (3818)

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Special interest databases

Plasmids’ maps:Syntax:

New FDS field: ‘External_links map <name>’

Links in place: Plasmids: LMBP (777)

Images of micro-organisms:Syntax:

New FDS field: ‘External_links image <name>’

Links in place: None (waiting for next catalogues’ update)

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Linking to EMBL (i)

• Linking “on-the-fly” 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)

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Linking to EMBL (ii)

(well known) Example of search “on-the-fly”:

• Searching for fil. fungi strain CBS 100.20Involves: 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*] )

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Linking to EMBL (iii)

• Agreement with EBI• Identification of crossreferences from CABRI

catalogues to EMBL (and viceversa) by unique IDs• Submission of the list to EBI• ID based links to CABRI included in EMBL data library

and distributed with it• Use these links when linking from CABRI

• Links from LMBP to EMBL managed differently

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Linking to EMBL (iv)

• Work started vs EMBL 79

• Common (new) SRS site for CABRI and EMBL• Modified indexing -> common keys format• SRS links established

• Preliminar list of references sent to collections• Comments returned

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Common site established

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Common keys format

CABRI indexing: by whole IDCBS 100.20 -> ‘CBS 100.20’

EMBL indexing: by single wordsCBS 100.20 -> ‘CBS’ + ‘100’ + ’20’

CBS100.20 -> ‘CBS100’ + ’20’

Common indexing: name (only letters), possibly followed by space, followed by string (including letters, numbers, dot, dash), punctuation removed

CBS 100.20 -> ‘CBS10020’

CBS100.20 -> ‘CBS10020’

Special case (not currently managed):

NCCB LMD and Phabagen bacteria catalogues

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SRS links EMBL - CABRI

#links Embl to Cabri Bact & Fun & Yeasts

$Link: [from:$EMBLRELEASE_DB to:$BCCM_LMG_DB fromField:$DF_FtDescription toField:$DF_CABRI_Strain_number]

$Link: [from:$EMBLRELEASE_DB to:$CBS_BACT_DB fromField:$DF_FtDescription toField:$DF_CABRI_Strain_number]

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Automatic identification of links

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Custom views (i)

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Custom views (ii)

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Links to EMBL: current status

Almost ready for submission of the list of crossreferences

EBI objection: many, some little, databases, instead of a big one

New proposal from EBILinks added in the SRS site at EBI only

Links not serchable

Links not distributed with EMBL Data Library

Alternative proposals from usMaking CABRI virtual catalogues by resource type (bacteria, cell lines,…)

Making an interrnediate database

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SRS virtual libraries

SRS Virtual librariesInclude many member libraries

Appear and can be searched as a unique database

Use indexes of member libraries

Member libraries must have a common data structure

CABRI Virtual librariesCan be created for each resource type

Interconnected Bacteria DB

Interconnected Cell Lines DB

May be created for similar resource typesInterconnected Micro-organisms DB

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Intermediate database

Intermediate CABRI database wouldInclude very limited infomation: identification and name

Be linked by EMBL and link to the related CABRI catalogueEMBL -> Intermediate db -> CABRI

Example:Identification CIP 70.34

Name Acinetobacter baumannii

Identification ECACC 88020401

Name Vero

Identification LMG 3589

Name Bacillus subtilis (Ehrenberg 1835) Cohn 1872 AL

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Extracted databases

• Intended to improve accessibility of CABRI catalogues by distributing them in a controlled frame

• Inlude a subset of information:CABRI MDS + link to CABRI site (new field Full_details)

• Established agreement with EBI• Preparation of extracted databases:

• Setting up of a purpose Web site: http://export.cabri.org/• Setting up of an FTP site for distributing data and SRS

configuration files: ftp.cabri.org (not anonymous) • Upload of catalogues to EBI: march 2004

• Automatic updating by FTP through SRS Prisma

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Catalogues at EBI

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CABRI views in place

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Link to CABRI for details & orders

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Quick searches at EBI (i)

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Quick searches at EBI (ii)

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Inventory of data usage and sets

• GlobalSearch on CABRI site available

• GlobalSearch on partners’ sites• Not stable• Partial (give me URLs!)

• Virtual BRCs’ Library• Map of sites’ maps• Includes links to archives/databases

• PLEASE SUBMIT YOUR DATA!

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That’all, folk!• MEDLINE

• Links to Medline already in place for many catalogues• New links added with periodical updates

• EMBL• Common site and index keys in place• Implementation of links under study with EBI staff

• Other external links• Plasmids’ maps in place• Micro-organisms images ongoing

• Extracted databases• Procedure implemented• Purpose web and ftp sites available• Uploaded to EBI march 2004

• Inventory of data usage and data sets• Search on partners’ site contents (ht://dig) soon available• List of partner’s site contents (sort of “Map of sites’ maps”) under construction

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Thoughts about the future (i)

• CABRI as it is• Many links to external databases are being set up and are already in place

for some of the catalogues• Extracted databases have been uploaded to EBI• Integration made possible (mainly) because of the adoption of SRS• CABRI sites are now well known, appreciated and use network services

• GBIF perspective• GBIF has designed a nice and innovative architecure• Distributed architecture can help management by avoiding conversions

and updates• It requires a sound expertise and good computer skills, not always

available at collections/BRCs• The ABCD Schema is not adequate for catalogues’ contents

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Thoughts about the future (ii)

• We need to keep current and set up new links• Current links with the molecular biology world should be kept

• SRS is an essential key for this connection

• Web Services based GBIF architecture must be taken into account for the future links with the (quickly) evolving biodiversity information environment

• SRS is evolving• Since SRS 6, XML has been incorporated

• With SRS 7, XML is essential (alternative to flat files)

• With SRS 8, Web Services have been added and SRS itself able to provide Web Services and to access them remotely

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Thoughts about the future (iii)

• Proposal• Start by extending the ABCD Schema to reach our needs

• Continue with SRS and follow its evolution

• Adopt as early as possible the new SRS Web Services features and start offering information to GBIF

• Individual collections/BRCs willing to go autonomous can stop submission of data, provided they offer an agreed interface for remote access by the central SRS based system

• Finally, reach a mix distributed/centralized architecture, based on SRS and offering both standard SRS services and Web Services