Difference between revisions of "TTO Changes"
From phenoscape
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Note: Obsoleting a term means it is no longer available for use and does not appear in the main hierarchy of the TTO. Phenoscape needs to retain the name and term id so that annotations to the term do not break. | Note: Obsoleting a term means it is no longer available for use and does not appear in the main hierarchy of the TTO. Phenoscape needs to retain the name and term id so that annotations to the term do not break. | ||
| − | * '''Family | + | * '''Family added''' A new TTO term is created, which should have a dbxref referring to the publication or some CoF derived identifier. |
* '''Family obsoleted''' The TTO term and id are obsoleted. Genera are moved to a new family or a higher taxon. | * '''Family obsoleted''' The TTO term and id are obsoleted. Genera are moved to a new family or a higher taxon. | ||
| − | * '''Genus | + | * '''Genus added''' A new TTO term is created, which should have a dbxref referring to the publication or a (new) CASGEN identifier |
* '''Genus obsoleted''' The TTO term and id are obsoleted. Any species under this genus are changed to the new genus. | * '''Genus obsoleted''' The TTO term and id are obsoleted. Any species under this genus are changed to the new genus. | ||
* '''Genus moved''' The existing genus has its is_a relation changed to point to the new family or higher taxon. | * '''Genus moved''' The existing genus has its is_a relation changed to point to the new family or higher taxon. | ||
| − | * '''Species | + | * '''Species added''' A new TTO term is created, which should have a dbxref referring to the publication or a (new) CASSPC identifier. |
* '''Species changed to/added as synonym of''' The TTO term and id are retained; the name is changed to the new name, the old name is added as a synonym. The is_a relation for the species is updated to the new genus. The synonym should have a dbxref refering to the publication. This is the default when the containing genus changes. | * '''Species changed to/added as synonym of''' The TTO term and id are retained; the name is changed to the new name, the old name is added as a synonym. The is_a relation for the species is updated to the new genus. The synonym should have a dbxref refering to the publication. This is the default when the containing genus changes. | ||
* '''Species obsoleted/added as synonym of ''' The term is obsoleted, the old name is added as a synonym of the new name. The CASSPC or other dbxref of the old term should be added to the synonym. This is the default when species are merged. | * '''Species obsoleted/added as synonym of ''' The term is obsoleted, the old name is added as a synonym of the new name. The CASSPC or other dbxref of the old term should be added to the synonym. This is the default when species are merged. | ||
Revision as of 23:55, 11 April 2008
Notes to the Reader
This is an overview of the possible actions for each change.
Note: Obsoleting a term means it is no longer available for use and does not appear in the main hierarchy of the TTO. Phenoscape needs to retain the name and term id so that annotations to the term do not break.
- Family added A new TTO term is created, which should have a dbxref referring to the publication or some CoF derived identifier.
- Family obsoleted The TTO term and id are obsoleted. Genera are moved to a new family or a higher taxon.
- Genus added A new TTO term is created, which should have a dbxref referring to the publication or a (new) CASGEN identifier
- Genus obsoleted The TTO term and id are obsoleted. Any species under this genus are changed to the new genus.
- Genus moved The existing genus has its is_a relation changed to point to the new family or higher taxon.
- Species added A new TTO term is created, which should have a dbxref referring to the publication or a (new) CASSPC identifier.
- Species changed to/added as synonym of The TTO term and id are retained; the name is changed to the new name, the old name is added as a synonym. The is_a relation for the species is updated to the new genus. The synonym should have a dbxref refering to the publication. This is the default when the containing genus changes.
- Species obsoleted/added as synonym of The term is obsoleted, the old name is added as a synonym of the new name. The CASSPC or other dbxref of the old term should be added to the synonym. This is the default when species are merged.
Changes resulting from invited update (April 2008) of Mayden and Conway
Notes: This update contains many subfamily assignments. We don't currently include subfamilies in the TTO, but the update file will be retained in case this policy changes.
- Paracanthocobitis added as synonym to Acanthocobitis
- Botiidae added as family
- Botia moved to family Botiidae
- Chromobotia moved to family Botiidae
- Leptobotia moved to family Botiidae
- Parabotia moved to family Botiidae
- Sinibotia moved to family Botiidae
- Syncrossus moved to family Botiidae
- Yasuhikotakia moved to family Botiidae
- Bibarba added as genus
- Erythroculter no change (unpublished suggestion to demote to synonym of Chandoichthys)
- Akrokolioplax no change (already in CoF)
- Henicorhynchus obsoleted/demoted to synonym of Bangana
- Henicorhynchus lobatus changed to/added as synonym of Bangana lobatus
- Henicorhynchus siamensis changed to/added as synonym of Bangana siamensis
- Henicorhynchus lineatus changed to/added as synonym of Bangana lineatus
- Henicorhynchus ornatipinnis changed to/added as synonym of Bangana ornatipinnis
- Acra changed so it is now a synonym of Bangana (was subgenus in CoF)
- Longiculter no change (uncertain subfamily change)
- Chalcalburnus obsoleted/demoted to synonym of Alburnus (as per online CoF) – no member species listed
- Psilorhynchoides obsoleted/demoted to synonym of Psilorhynchus
- Psilorhynchoides pseudecheneis changed to /demoted to synonym of Psilorhynchus pseudecheneis
- Psilorhynchoides arunachalensis changed to/demoted to synonym of Psilorhynchus arunachalensis
- Psilorhyncus robustus added as species
- Celesteichthys obsoleted/demoted to synonym of Danio
- Celesteichthys margaritatus changed to/added as synonym of Danio margaritatus
- Bengala demoted to synonym of Megarasbora
- Bengala elanga changed to/demoted to synonym of Megarasbora elanga
- Cyprinopsis no change, problem appears in description date, not covered in TTO
- Mirolabeo no change, uncertain demotion to synonym of Bangana
- Vaillantellidae added as family
- Vaillantella moved to family Vaillantellidae
- Caucus – appears as cypriniform in online CoF, but was not in CAS species table so never added to TTO; after consultation recommendation was to remove/not add; no change.
- Oreodaimon – appears as synonym to Pseudolabrus in online CoF, no change.
- Orthrias barbatulus zetensis no change (already demoted in CoF)
- Schistura cryptofasciata no change (already in CoF)
- Notropis harperi changed to/demoted to synonym of Pteronotropis harperi
- Microrasbora micropthalma added as species
- Araiocypris added as genus to Cyprinidae
- Araiocypris batodes added as species
