CABRI

1
CABRI EBRCN Web sitesCurrent status and
developments

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• Paolo Romano

2
CABRI site current status (I)

• New catalogues
• NCIMB bacteria catalogue (6,923 strains) on the
  main site and mirrors
• NCIMB phages and plamids catalogues on the test
  site
• Phages 69 strains, waiting for final test by
  NCIMB
• Plasmids 127 elements, waiting for final
  approval by CABRI-TC

3
CABRI site current status (II)

• Update of catalogues
• Catalogues should be updated at least once a year
• Since Utrecht we had 3 deadlines
• May 2002 Fungi and Yeastssubmitted CBS and
  CABI, updated CBS filamentous fungi
• July 2002 Cell lines and Plasmidssubmitted ICLC
  animal cells, updated ICLC
• September 2002 Bacteriasubmitted LMG, NCIMB,
  NCCB and CABI, updated LMG, NCIMBunified NCCB
  (available in the main site only for
  HyperCatalogue)
• November 2002 random updatesubmitted ICLC,
  updated ICLC (Literature links)

4
Indexing of flat files

• Improvements in indexing of flat files
• Catalogues must further converge to a common
  syntax
• Needed corrections notified to collections before
  updates
• Focus on fields Name, Other_collection_numbers,
  Literature
• Improved indexing of Other_collection_numbers
  supporting identification of duplications

5
Indexing of flat files (II)

• 3 links in place for each pair of catalogues (on
  SRS 6)
• from Strain_number to Other_collection_numbers
• from Other_collection_numbers to Strain_number
• from Other_collection_numbers to
  Other_collection_numbers
• Strains in CIP which are also in DSMZ bacteria
  collection
• ((( cip_bact lt ( cip_bact_el lt
  dsmz_bact_el ))
• ( cip_bact lt ( cip_bact_rl lt dsmz_bact_rl
  )))
• ( cip_bact lt dsmz_bact ))
• Test on http//srs.cabri.org/srs6/, using
  Results section

6
Catalogue guidelines

• Revision of catalogue production guidelines
• Evolve as new data fields are defined (EBRCN/WP4)
• New Flat file preparation guide (ver 5, Oct 7,
  2002)
• Revised MDS descriptions for animal cells,
  bacteria, fungi and yeasts, plasmids, phages,
  genetic libraries (added Field_label column)
• Revised Data input procedure for animal cells
  (added PMID to Literature)

7
Developments hits number

• Simple search returning number of hits
• Two approaches presented and discussed in
  Utrecht
• All searches carried out (slower at first, faster
  retrieval of results of single catalogues)
• Only count of hits carried out (faster at first,
  implies that searches are carried out during
  following retrievals)

8
Developments hits number

• New implementation of the fastest solution
• execute global query,
• count hits in SRS session file user.par(1),
• return hits figures,
• retrieve results for global query,
• execute single or multiple queries upon request
• (1) Problems with Linux SRS 5.1

9
Developments hits number

• Three variants available online for testing
• A http//www.cabri.org/CABRI/cabri-srs-doc/index-h
  its.html
• B http//www.cabri.org/CABRI/cabri-srs-doc/index2.
  html
• C http//www.cabri.org/CABRI/cabri-srs-doc/new-ind
  ex-hits.html
• Test simple search, all bacteria catalogue,
  name acetobacter
• A and B 12 seconds
• C 3 seconds

10
Developments HyperCatalogue

• CABRI HyperCatalogue
• A hypertext including a set of static HTML
  indexes links to local SRS for retrieval of
  full entries
• ca. 48,000 HTML files and ca. 92 Mbytes
• Flat files -gt Relational DB -gt HTML
• MySQL, perl PHP
• Revised indexes (plasmids), reduced files size
• Available online on main site and mirrors since
  Nov 2002 http//www.cabri.org/HyperCat/

11
Developments GlobalSearch

• CABRI GlobalSearch
• Free text search engine for CABRI web site
• Search on sections of the site (eg, Guidelines,
  HyperCatalogue)
• Based on ht//Dig public software
• Available online for testing on devoted
  sitehttp//htdig.cabri.org/
• Could be used to index all partners site and
  search their contents in a unique step (only
  static files, not searchable archives)

12
Developments SRS 6

• Testing SRS 6
• SRS 6 still under evaluation
• Quick Search as a substitute for simple search(
  ( bacillus AND subtilis ) OR bacillus
  subtilis )is simpler and more effective
• SRS Internal links by link operators satisfying
  and used for identifying duplications of strains
• Synonyms searches not practical either
  re-implement simple search or find an alternative
• The same for the shopping cart
• On-going revision of structure of reference files
  for SRS 6

13
Developments SRS 6 (and 7)

• SRS 7 soon available
• o Is going to substitute previous versions
• o It is said to offer an improved support for XML
• o License already required by INRC
• So what?
• o Further postpone decision on substitution of
  SRS 5.1
• o Short stay in Cambridge
• o Use SRS 7 instead of SRS 6

14
Developments Mirrors

• CABRI Mirrors
• Chinese mirror implemented
• http//www.cn.cabri.org/
• Mirror added to list on main site and mirrors
• General mirroring issues
• Simplified implementation by new procedure and
  guide available on ftp.cabri.org, user cabri-dl
• Mirrors must provide log files more regularly

15
CABRI Site Contents

• Contents
• Editorial board same as EBRCN?
• New public documents section?
• Experts for answering questions from users?
• Multilingual implementation delayed after
  launching of EBRCN web site

16
CABRI Site Visibility

• Visibility through search engines
• HyperCatalogue GlobalSearch recently added,
  impact not yet determined
• Registration in directories
• added SRS 6 version in the list of publicly
  available SRS 6 sites (http//downloads.lionbio.co
  .uk/publicsrs.html)
• survey on inclusion in directories Altavista
  gave 229 hits for linkcabri.org and not
  urlcabri.org and not urlebrcn.org
• analysis of logs 14.37 hits from search engines
  and directories in november 2002

17
CABRI Site Awareness

• Announcements on mailing lists,
  newsgroupsprovide a list
• EBRCN Newsletter
• Scientific journals papersCoordinated
  approaches to the management of biotechnology
  resources, as it relates to bioinformatics,
  invited survey for Applied Bioinformatics (in
  preparation)

18
Site hits total, main site
19
Site hits home page, main site
20
Site hits searches vs guidelines
21
Site hits main site vs mirrors
Total hits september and october 2002
22
EBRCN site Management

• Site management
• Site contents is now built on the fly from
  database
• Added procedures for contents insertion and
  translation
• Five access levels
• admin, author, translator, proofreader, observator

23
EBRCN site Management

• Administrator (A) Can do anything.The only one
  who is able to delete and to publish.
• Author (W,EN) Writes new and modifies existing
  texts in English only
• Author and translator (W,IT/FR/DE) Like Author,
  but can also translate into his own language
• Translator (T,IT/FR/DE) Translates from English
  into his own language
• Proofreader (T) Can modify existing texts in any
  language
• Observator (O) Cant carry out any change

24
EBRCN site contents

• Contents agreed upon in Heraklion and Utrecht
• User/password pairs defined for partners for
  restricted area
• Workshop abstracts and meeting minutes added in
  the restricted area
• Meeting minutes added, not sent by email
• Regular submission of events and news
• Slight changes were introduced
• Added Newsletter section
• Added newsletter and newsletter-t mailing list
• Added newsletter subscription form data recorded
  in database and sent to list owner

25
EBRCN site contents

• What next
• Editorial board defined in UtrechtHominick,
  Dutertre, Gleim, Romano and Malanda
• Languages and translators defined in
  UtrechtEnglish (reference), Italian, French,
  German
• Contents checked by Béatrice Dutertre and amended
• Translation in french done and available
• Translation in german done, not yet on the site
• Translation in italian on-going