SABIO-RK database and software updates

Software v. 2.29

11/21/22

- Bar Chart Search: adding UniProtID's
- Bar Chart Search: adding cellular locations
- bug fixes

Software v. 2.28

8/9/22

- visual search for kinetic parameters implemented
- bugs fixed

Software v. 2.27

3/2/22

- Python web services: added date of data insertion as output field
- Python web services: search for date range of data insertion

Database v. 2.18

2/22/22

- new publications added

Software v. 2.26

12/28/21

- check log4j security vulnerability
- rounding of numbers improved (less positions after decimal point)
- functionality for a Python script for pathway search and pathway synonyms
- integration of more pathway synonym names
- functionality for a Python script for export of enzyme synomym names
- bug fixes:
- RESTful webservices reduced functionality during transfer procedure
- validation of ECnumbers extended for 7.x
- conversion of values to SI units

Database v. 2.17

12/20/21

- new publications added

Software v. 2.25

10/5/21

- bug fixes

Database v. 2.16

10/4/21

- new publications added

Database v. 2.15

8/6/21

- new publications added

Database v. 2.14

5/28/21

- new publications added

Software v. 2.24

5/11/21

- visual search tab: replacement of Google visualization JS API by D3JS API
- new EnyzmeML validation template

Software v. 2.23

4/21/21

- fixed bug for querying ions like Fe2+; observed in Google Chrome on Ubuntu

Software v. 2.22

3/15/21

- fixed bug in RESTFul web services Python Script #1 for case that no matching entries are found
- added JSON file of EnzymeML validation for download

Software v. 2.21

3/9/21

- export functionality added for ReactomeReactionID field in RESTFul web services

Software v. 2.20

3/1/21

- BTO BRENDA link update
- fixed bug in advanced search for positively charged ions like 'Fe2+', 'Na+'

Database v. 2.13

2/7/21

- new publications added

Software v. 2.19

1/12/21

- external links for enzyme references to ExPASy and IUBMB updated
- web services: added another example Python script including SBML export
- SBML export: wrong Uniprot annotation link corrected
- Solr query with Boolean 'or' resulted in restricted resultset by default -> fixed

Database v. 2.12

12/16/20

- new publications added
- updated mapping to MetaNetX, KEGG, ChEBI, MetaCyc, Rhea, Pubchem

Software v. 2.18

11/19/20

- restriction on query with many Boolean 'or' operators overriden
- dynamic functionality for information on server downtime added
- displays prominent link for de.NBI user evaluation form (smileys)
- SBML export: missing link to original source other than Pubmed added

Software v. 2.17

9/21/20

- bug fixed calculation / selection in advanced search

Software v. 2.16

9/8/20

- bug fixed display of data on visual search tab
- filter added for contact form
- SBML export: link to original source (non-Pubmed)

Software v. 2.15

8/3/20

- bug fixed on contact form forwarding
- bug fixed JSON output: escape backslash with double backslash

Software v. 2.14

6/30/20

- search for synonym pathway names
- bug fixed in RESTful services: sabioRestWebServices/suggestions eg http://sabio.h-its.org/sabioRestWebServices/suggestions/Tissues?searchTissues=lu
- method implemented for retrieval of JSON objects by PubMed ID: http://sabio.h-its.org/entry/getJSONentriesByPubMedId?pubmedId=7437446&printPretty=true
- visualization of retrieved data as graphs eg organisms, tissues, EC-numbers,...

Database v. 2.11

6/29/20

- new publications added

Database v. 2.09

9/20/19

- new publications added

Software v. 2.13

7/9/19

- new page for protein details
- common style for all details pages
- linking to Biomodels

Database v. 2.08

4/11/19

- tables added for external links including Rhea reaction, Reactome reaction, MetaCyc reaction, MetaNetX reaction, Uniprot Omim, KEGG pathway
- new publications added

Software v. 2.12

4/11/19

- search functionality added for Rhea reaction, Reactome reaction, MetaCyc reaction, MetaNetX reaction, Uniprot Omim, KEGG pathway
- implementation of URL-mediated search encoded by links eg http://sabiork.h-its.org/newSearch?q=Organism:"Plasmodium falciparum" AND ECNumber:"4.2.1.11"
- implemented: usage of synonyms in advanced search tab eg "human" instead of "homo sapiens"
- fixed: "Reset" button did not always work

Software v. 2.11

12/10/18

- new web service method implemented: returns reaction modifier details
- bug fixed in web service method 'searchReactionParticipants'
- added cross-linking of compounds to: MetaCyc, MetaNetX, Reactome
- implementation of Bioschemas semantic markup

Database v. 2.07

10/10/18

- new publications included

Software v. 2.09

8/7/18

- added search facilities for BTO / NCBI terms in advanced search fields
- RESTful webservices: speed of response time for getSuggestions method highly increased by implementation of data caching

Software v. 2.08

6/11/18

- added functionality for linking to Cellosaurus (https://web.expasy.org/cellosaurus/); eg search for: hek-293 cell
- according to the EU-DSGVO, the linking to the HITS general HITS privacy / imprint policy was adjusted

Database v. 2.06

5/2/18

- new publications included

Software v. 2.07

4/23/18

- added search facilities for tissue synonyms
- added search facilities for organism synonyms
- added search facilities for dellular location synonyms
- added search facilities for SMILES string
- regular expression for new 10-digit UniportIDs updated
- added link to ChemSpider
- web-services: added search facilities for BTO
- web-services: added search facilities for NCBI
- web services: add methods to get database /software release info

Database v. 2.05

3/23/18

- new publications included
- direct submissions from STRENDA DB

Software v. 2.06

2/26/18

- output fields added for web services (tsv format) eg ChebiID
- output of big result sets (> 10000)
- additional single-step method for tsv output

Database v. 2.04

2/17/18

- new publications included
- NCBI taxonomy updated

Database v. 2.03

1/31/18

- new publications included
- content errors corrected

Software v. 2.05

11/13/17

- alternative export formats (Matlab, BioPAX level 2 and 3, ...) access by web services
- bug fix in SBML annotation syntax
- update web services manual

Software v. 2.04

11/8/17

- added BTO identifier in SBML output for tissue description in reaction annotation
- added export functionality for APM, DOT and SBGNML
- improved, corrected & extended manual for web services
- some bug fixing

Software v. 2.03

10/13/17

- added export functionality for BioPax level 2 and 3, Matlab, Octave, XPP
- update of links, publications, documentation
- outdated Adobe Flash used on statistics page replaced by Javascript
- some bug fixing

Database v. 2.02

5/19/17

- new publications included
- content errors corrected

Software v. 2.02

5/19/17

- framework implemented for automatic transfer procedure
- bug fix on webservices permissions

Software v. 2.01

2/21/17

- start of public SABIO-RK versioning
- CRUD interface for versioning implemented
- new video tutorials added

Database v. 2.01

2/17/17

- start of public SABIO-RK versioning
- newly curated data made accessible to the public
- about 55800 single entries accessible