Release Notes
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Current release
Omnicrobe 1.6
(current release)
Information about the data
- Ontologies used: OntoBiotope version 2022-04-28 & Taxonomy version 2024-10-21.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2024-07-15 | 2024-10-21 | 2024-10-21 | 2024-10 | 2024-10 | 2022-10-14 |
| Taxa - Habitat relations | 660,828 | 275,343 | 53,613 | 789 | 1,429 | 925 |
| Taxa - Phenotype relations | 47,639 | - | - | - | - | - |
| Taxa - Use relations | 14,923 | - | - | - | - | - |
New features and improvements in this release
- improved extraction quality
- improved taxon name disambiguation
- fixed bugs
- updated taxonomy
- updated PubMed, GenBank and DSMZ data
Previous releases
Omnicrobe 1.5
Information about the data
- Ontologies used: OntoBiotope version 2022-04-28 & Taxonomy version 2024-04-18.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2024-04-18 | 2024-04-18 | 2024-04-18 | 2023-03-09 | 2023-03-16 | 2022-10-14 |
| Taxa - Habitat relations | 628,173 | 296,517 | 53,616 | 707 | 1,125 | 936 |
| Taxa - Phenotype relations | 45,408 | - | - | - | - | - |
| Taxa - Use relations | 14,169 | - | - | - | - | - |
New features and improvements in this release
- improved API features:
- gather taxon id information from taxon name [/get/taxons/{name}]
- no case sensitivity on searches [/search/taxon;/search/obt]
- limit the relations in a given document [/search/relations]
- return several URL for the PubMed record [/get/doc/{source}/{docid}]
- return several URL for the NCBI taxon [/get/taxon/{taxid};/get/taxons/{name}]
Omnicrobe 1.4
Information about the data
- Ontologies used: OntoBiotope version 2022-04-28 & Taxonomy version 2024-04-18.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2024-04-18 | 2024-04-18 | 2024-04-18 | 2023-03-09 | 2023-03-16 | 2022-10-14 |
| Taxa - Habitat relations | 628,173 | 296,517 | 53,616 | 707 | 1,125 | 936 |
| Taxa - Phenotype relations | 45,408 | - | - | - | - | - |
| Taxa - Use relations | 14,169 | - | - | - | - | - |
New features and improvements in this release
- improved extraction quality
- improved taxon name disambiguation
- fixed bugs
- updated taxonomy
- updated PubMed, GenBank and DSMZ data
Omnicrobe 1.3
Information about the data
- Ontologies used: OntoBiotope version 2022-04-28 & Taxonomy version 2023-10-09.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2023-10-09 | 2023-10-15 | 2023-10-09 | 2023-03-09 | 2023-03-16 | 2022-10-14 |
| Taxa - Habitat relations | 623,402 | 274,053 | 51,170 | 677 | 1,216 | 930 |
| Taxa - Phenotype relations | 45,158 | - | - | - | - | - |
| Taxa - Use relations | 14,118 | - | - | - | - | - |
New features and improvements in this release
- improved extraction quality
- fixed bugs
- updated taxonomy
Omnicrobe 1.2
Information about the data
- Ontologies used: OntoBiotope version 2022-04-28 & Taxonomy version 2023-02-24.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2023-03-27 | 2023-03-27 | 2023-03-27 | 2023-02-09 | 2023-03-16 | 2022-10-14 |
| Taxa - Habitat relations | 764,796 | 268,781 | 51,176 | 682 | 1,223 | 942 |
| Taxa - Phenotype relations | 53,377 | - | - | - | - | - |
| Taxa - Use relations | 18,145 | - | - | - | - | - |
New features and improvements in this release
- improved extraction quality
- fixed bugs
- updated taxonomy
Omnicrobe 1.1
Information about the data
- Ontologies used: OntoBiotope version 2022-04-28 & Taxonomy version 2022-10-21.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2022-10-07 | 2022-10-26 | 2022-10-26 | 2022-09-30 | 2022-10-07 | 2022-10-14 |
| Taxa - Habitat relations | 731,066 | 266,417 | 50,499 | 669 | 1,337 | 941 |
| Taxa - Phenotype relations | 51,216 | - | - | - | - | - |
| Taxa - Use relations | 17,225 | - | - | - | - | - |
New features and improvements in this release
- improved extraction quality
- fixed bugs
- updated taxonomy
Omnicrobe 1.0
Information about the data
- Ontologies used: OntoBiotope version 2022-04-22 & Taxonomy version 2022-04-13.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2022-04-10 | 2022-04-22 | 2018-01-26 | 2021-03-07 | 2022-03-08 | 2021-08-23 |
| Taxa - Habitat relations | 721,244 | 259,745 | 35,696 | 604 | 1,109 | 943 |
| Taxa - Phenotype relations | 50,410 | - | - | - | - | - |
| Taxa - Use relations | 16,007 | - | - | - | - | - |
New features and improvements in this release
- improved extraction quality
- fixed bugs
- updated taxonomy
- updated OntoBiotope
Omnicrobe 0.2
Information about the data
- Ontologies used: OntoBiotope version 2021-10-22 & Taxonomy version 2021-10-21.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2021-08-11 | 2021-09-20 | 2018-01-26 | 2021-07-20 | 2020-09-22 | 2021-08-23 |
| Taxa - Habitat relations | 683,016 | 255,855 | 15,865 | 580 | 897 | 966 |
| Taxa - Phenotype relations | 53,996 | - | - | - | - | - |
| Taxa - Use relations | 14,620 | - | - | - | - | - |
New features and improvements in this release
- Uses the Extended microorganisms taxonomy
- Several fixes on ambiguous habitat detection
- Improved detection of strain names and strain numbers
Omnicrobe 0.1
Information about the data
- Ontologies used: OntoBiotope version 2021-09-17 & Taxonomy version 2021-08-17.
| PubMed | GenBank | DSMZ | CIRM-BIA | CIRM-CFBP | CIRM-Levures | |
|---|---|---|---|---|---|---|
| Version | 2021-08-11 | 2021-09-20 | 2018-01-26 | 2021-07-20 | 2020-09-22 | 2021-08-23 |
| Taxa - Habitat relations | 681,806 | 256,081 | 35,799 | 510 | 184 | 964 |
| Taxa - Phenotype relations | 53,156 | - | - | - | - | - |
| Taxa - Use relations | 14,381 | - | - | - | - | - |
New features and improvements in this release
- Adding CIRM-CFBP data