1. EBRCN General Meeting, Genova, 26-28/03/20031 CABRI Web sites On going 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, Genova, 26-28/03/2003 2 CABRI site: current status (I) New catalogues NCIMB phages catalogue (69 strains) on the main site and mirrors NCIMB plamids catalogues (127 elements) still on the test site, waiting for final approval by CABRI- TC

3. EBRCN General Meeting, Genova, 26-28/03/2003 3 CABRI site: current status (II) Update of catalogues Catalogues should be updated at least once a year Since Paris we had 3 deadlines: January 2003: animal cell lines and plasmids submitted and updated BCCM/LMBP (Literature links) February 2003: other catalogues none submitted March 2003: bacteria none submitted

4. EBRCN General Meeting, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 6 Catalogue guidelines Revision of catalogue production guidelines 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 procedures for bacteria, fungi and yeasts, plasmids, phages (added PMID to Literature)

7. EBRCN General Meeting, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 14 CABRI Site: Contents (i) Site Map Better visibility of the contents (e.g., prices, guides) Faster accessibility to the site (two clicks) Not all contents linked, just meaningful points

15. EBRCN General Meeting, Genova, 26-28/03/2003 15 CABRI Site: Contents (ii) FAQ (Frequently Asked Questions) Not only frequently asked questions Overview of the objectives Sections on: What is CABRI CABRI and EBRCN Ordering procedures Searching procedures Copyrights Suggestions welcome!

16. EBRCN General Meeting, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 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, Genova, 26-28/03/2003 18 Site hits: total, main site

19. EBRCN General Meeting, Genova, 26-28/03/2003 19 Site hits: home page, main site

20. EBRCN General Meeting, Genova, 26-28/03/2003 20 Site hits: searches vs guidelines

21. EBRCN General Meeting, Genova, 26-28/03/2003 21 Site hits: main site vs mirrors Total hits september and october 2002