EBRCN General Meeting, Paris, 28-29/11/2002 1

CABRI & EBRCN Web sites

Current 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:

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

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 availableo 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 implementedo http://www.cn.cabri.org/

• Mirror added to list on main site and mirrors

• General mirroring issueso Simplified implementation by new procedure and

guide available on ftp.cabri.org, user cabri-dlo 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

0

5.000

10.000

15.000

20.000

25.000

30.000

35.000

40.000

45.000

50.000

1101

1201

0102

0202

0302

0402

0502

0602

0702

0802

0902

1002

EBRCN General Meeting, Paris, 28-29/11/2002 19

Site hits: home page, main site

0

200

400

600

800

1.000

1.200

1.400

1.600

1.800

2.000

11 01 12 01 01 02 02 02 03 02 04 02 05 02 06 02 07 02 08 02 09 02 10 02

EBRCN General Meeting, Paris, 28-29/11/2002 20

Site hits: searches vs guidelines

0

5.000

10.000

15.000

20.000

25.000

30.000

1101

1201

0102

0202

0302

0402

0502

0602

0702

0802

0902

1002

Home Guidelines Searches

EBRCN General Meeting, Paris, 28-29/11/2002 21

Site hits: main site vs mirrors

MAIN 85.404 94,92%BE 2.495 2,77%IT 846 0,94%FR 660 0,73%SRS 567 0,63%

TOTAL 89.972 100,00%

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