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CABRI & EBRCN Web sites Current status and developments

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CABRI & EBRCN Web sites Current status and developments

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  1. 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. CABRI & EBRCN Web sitesCurrent status and developments Paolo Romano 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 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 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) 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 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” section 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) • 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) 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) EBRCN General Meeting, Paris, 28-29/11/2002

  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 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.html B http://www.cabri.org/CABRI/cabri-srs-doc/index2.html C http://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 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/ 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/ • Could be used to index all partners’ site and search their contents in a unique step (only static files, not searchable archives) 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 EBRCN General Meeting, Paris, 28-29/11/2002

  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 EBRCN General Meeting, Paris, 28-29/11/2002

  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 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 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) • 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 EBRCN General Meeting, Paris, 28-29/11/2002

  17. CABRI Site: Awareness • Announcements on mailing lists, newsgroupsprovide 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) EBRCN General Meeting, Paris, 28-29/11/2002

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

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

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

  21. Site hits: main site vs mirrors Total hits september and october 2002 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 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): Can’t carry out any change 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 EBRCN General Meeting, Paris, 28-29/11/2002

  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 EBRCN General Meeting, Paris, 28-29/11/2002

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