1. EBRCN General Meeting, Paris, 28-29/11/20021 CABRI & EBRCN Web sites Current status and developments Paolo Romano 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.

2. EBRCN General Meeting, Paris, 28-29/11/2002 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. EBRCN General Meeting, Paris, 28-29/11/2002 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 Yeasts submitted: CBS and CABI, updated CBS filamentous fungi July 2002: Cell lines and Plasmids submitted ICLC animal cells, updated ICLC September 2002: Bacteria submitted LMG, NCIMB, NCCB and CABI, updated LMG, NCIMB unified: NCCB (available in the main site only for HyperCatalogue) November 2002: random update submitted ICLC, updated ICLC (Literature links)

4. EBRCN General Meeting, Paris, 28-29/11/2002 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. EBRCN General Meeting, Paris, 28-29/11/2002 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 < ( cip_bact_el < dsmz_bact_el )) | ( cip_bact < ( cip_bact_rl < dsmz_bact_rl ))) | ( cip_bact < dsmz_bact )) Test on http://srs.cabri.org/srs6/, using Results sectionhttp://srs.cabri.org/srs6/

6. EBRCN General Meeting, Paris, 28-29/11/2002 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)Flat file preparation 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. EBRCN General Meeting, Paris, 28-29/11/2002 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. EBRCN General Meeting, Paris, 28-29/11/2002 8 Developments: hits number New implementation of the fastest solution: 1.execute global query, 2.count hits in SRS session file user.par (1), 3.return hits figures, 4.retrieve results for global query, 5.execute single or multiple queries upon request (1) Problems with Linux & SRS 5.1

9. EBRCN General Meeting, Paris, 28-29/11/2002 9 Developments: hits number Three variants available online for testing: A http://www.cabri.org/CABRI/cabri-srs-doc/index-hits.htmlhttp://www.cabri.org/CABRI/cabri-srs-doc/index-hits.html B http://www.cabri.org/CABRI/cabri-srs-doc/index2.htmlhttp://www.cabri.org/CABRI/cabri-srs-doc/index2.html C http://www.cabri.org/CABRI/cabri-srs-doc/new-index-hits.htmlhttp://www.cabri.org/CABRI/cabri-srs-doc/new-index-hits.html Test: simple search, all bacteria catalogue, name: acetobacter* A and B: 12 seconds C: 3 seconds

10. EBRCN General Meeting, Paris, 28-29/11/2002 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 -> Relational DB -> 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/http://www.cabri.org/HyperCat/

11. EBRCN General Meeting, Paris, 28-29/11/2002 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 site: http://htdig.cabri.org/ http://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. EBRCN General Meeting, Paris, 28-29/11/2002 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. EBRCN General Meeting, Paris, 28-29/11/2002 13 Developments: SRS 6 (and 7) SRS 7 soon available oIs going to substitute previous versions oIt is said to offer an improved support for XML oLicense already required by INRC So what? oFurther postpone decision on substitution of SRS 5.1 oShort stay in Cambridge oUse SRS 7 instead of SRS 6

14. EBRCN General Meeting, Paris, 28-29/11/2002 14 Developments: Mirrors CABRI Mirrors Chinese mirror implemented ohttp://www.cn.cabri.org/http://www.cn.cabri.org/ Mirror added to list on main site and mirrors General mirroring issues oSimplified implementation by new procedure and guide available on ftp.cabri.org, user cabri-dl oMirrors must provide log files more regularly

15. EBRCN General Meeting, Paris, 28-29/11/2002 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. EBRCN General Meeting, Paris, 28-29/11/2002 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)http://downloads.lionbio.co.uk/publicsrs.html survey on inclusion in directories: Altavista gave 229 hits for link:cabri.org and not url:cabri.org and not url:ebrcn.org analysis of logs: 14.37% hits from search engines and directories in november 2002

17. EBRCN General Meeting, Paris, 28-29/11/2002 17 CABRI Site: Awareness Announcements on mailing lists, newsgroups provide a list EBRCN Newsletter Scientific journals papers Coordinated approaches to the management of biotechnology resources, as it relates to bioinformatics, invited survey for Applied Bioinformatics (in preparation)

18. EBRCN General Meeting, Paris, 28-29/11/2002 18 Site hits: total, main site

19. EBRCN General Meeting, Paris, 28-29/11/2002 19 Site hits: home page, main site

20. EBRCN General Meeting, Paris, 28-29/11/2002 20 Site hits: searches vs guidelines

21. EBRCN General Meeting, Paris, 28-29/11/2002 21 Site hits: main site vs mirrors Total hits september and october 2002

22. EBRCN General Meeting, Paris, 28-29/11/2002 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 General Meeting, Paris, 28-29/11/2002 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 General Meeting, Paris, 28-29/11/2002 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 General Meeting, Paris, 28-29/11/2002 25 EBRCN site: contents What next Editorial board defined in Utrecht Hominick, Dutertre, Gleim, Romano and Malanda Languages and translators defined in Utrecht English (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