Difference between revisions of "Hackathon 2013/UseCases"
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===Doing revisionary taxonomy & systematics=== | ===Doing revisionary taxonomy & systematics=== | ||
− | * '''Background''': Taxonomic revisions, cladistic analyses and developing classifications require. | + | * '''Background''': Taxonomic revisions, cladistic analyses and developing classifications require integrate additional and more complex data. In TaxonWorks, the core concept of species is relaxed into two conceptual entities: the OTU and the taxonomic hypothesis. |
* '''Approach''': | * '''Approach''': | ||
* '''Challenges''': | * '''Challenges''': | ||
+ | ** Use trees as a method of batch import/export of OTUs and hypotheses | ||
+ | ** Can we make a fully marked-up tree in NeXML that has nodes annotated with, for example, clade names, informational tags, bootstrap values, importable into TaxonWorks? | ||
+ | *** These imported annotations should be propagated out as tags to everything (every OTU?) that inherits from a node, based on the hierarchy. | ||
+ | **** Question: is this going to litter the world with tags everywhere? | ||
+ | **** Will these tags be able to be used as characters associated with entities in their own right? | ||
** Advanced nomenclatural handling | ** Advanced nomenclatural handling | ||
** Multiple hierarchies | ** Multiple hierarchies | ||
Line 68: | Line 73: | ||
== Considerations for making a systematist-friendly taxonomic workbench == | == Considerations for making a systematist-friendly taxonomic workbench == | ||
− | * In TaxonWorks, the core concept of species is relaxed into two conceptual entities: the OTU and the taxonomic hypothesis. | + | *In TaxonWorks, the core concept of species is relaxed into two conceptual entities: the OTU and the taxonomic hypothesis. |
** OTUs represent either specimens or groups of specimens? | ** OTUs represent either specimens or groups of specimens? | ||
** A taxonomic hypothesis is either itself an OTU or a collection of OTUs? | ** A taxonomic hypothesis is either itself an OTU or a collection of OTUs? | ||
* It would be very helpful if trees themselves could be used as a method of batch import/export of OTUs and hypotheses: | * It would be very helpful if trees themselves could be used as a method of batch import/export of OTUs and hypotheses: | ||
** If one created a fully marked-up tree in NeXML that had nodes annotated with, for example, clade names, informational tags, bootstrap values, that should be importable into TaxonWorks. | ** If one created a fully marked-up tree in NeXML that had nodes annotated with, for example, clade names, informational tags, bootstrap values, that should be importable into TaxonWorks. | ||
− | ** These imported annotations should be propagated out as tags to everything (every OTU?) that inherits from a node, based on the hierarchy. | + | *** These imported annotations should be propagated out as tags to everything (every OTU?) that inherits from a node, based on the hierarchy. |
− | *** Question: is this going to litter the world with tags everywhere? | + | **** Question: is this going to litter the world with tags everywhere? |
− | *** Will these tags be able to be used as characters associated with entities in their own right? | + | **** Will these tags be able to be used as characters associated with entities in their own right? |
+ | |||
== Implementation plan and milestones == | == Implementation plan and milestones == |
Revision as of 10:46, 3 October 2013
Contents |
Members
- Daisie Huang
- David Eades
- Marilyn Beckman
Topics to be covered
- Use cases, identify types of users and what we must deliver.
- Define implementation plan and milestones.
- Map imports from Species Files, MX and 3i into TaxonWorks.
Use cases
Describing a new species
- Background:
- With estimates of 10-20,000 new species being described every year, there is a need for tools to facilitate alpha taxonomy. Taxonomists will be able to use TW as a starting point for research.
- Approach
- Challenges:
- Existing hierarchy with nomenclatural data
- References to relevant literature
- Added information: specimen data, images, sound recordings
- Assistance during research
- Generate private copy with relevant scope
- Add data in database
- Manage characters including molecular
- Handle OTUs in flux
- Export text to drop in manuscript
- Upon publication
- Merge private copy into public database
- Preconditions
- Steps
Doing revisionary taxonomy & systematics
- Background: Taxonomic revisions, cladistic analyses and developing classifications require integrate additional and more complex data. In TaxonWorks, the core concept of species is relaxed into two conceptual entities: the OTU and the taxonomic hypothesis.
- Approach:
- Challenges:
- Use trees as a method of batch import/export of OTUs and hypotheses
- Can we make a fully marked-up tree in NeXML that has nodes annotated with, for example, clade names, informational tags, bootstrap values, importable into TaxonWorks?
- These imported annotations should be propagated out as tags to everything (every OTU?) that inherits from a node, based on the hierarchy.
- Question: is this going to litter the world with tags everywhere?
- Will these tags be able to be used as characters associated with entities in their own right?
- These imported annotations should be propagated out as tags to everything (every OTU?) that inherits from a node, based on the hierarchy.
- Advanced nomenclatural handling
- Multiple hierarchies
- Preconditions
- Steps
Modeling the biogeography of a family
- Background:
- Approach:
- Challenges:
- Specimens on maps
Researching coevolutionary relationships
- Background:
- Approach:
- Challenges:
Facilitate data exchange with data aggregators
- Background:
- Challenges:
- Import and Export DwC-A
- to Catalogue of Life and ITIS
- Develop data exchange with GBIF, ZooBank, others
- Web service clients
- Handles requests for hierarchy
- Inquiries about status of names
- Participate in attempts to resolve conflicts with Catalogue of Life Piping Tool
Maintain a useful and user friendly web interface
- Background:
- Challenges:
- Display data in user friendly form
- Facilitate querying of Collections data at Illinois Natural History Survey
Considerations for making a systematist-friendly taxonomic workbench
- In TaxonWorks, the core concept of species is relaxed into two conceptual entities: the OTU and the taxonomic hypothesis.
- OTUs represent either specimens or groups of specimens?
- A taxonomic hypothesis is either itself an OTU or a collection of OTUs?
- It would be very helpful if trees themselves could be used as a method of batch import/export of OTUs and hypotheses:
- If one created a fully marked-up tree in NeXML that had nodes annotated with, for example, clade names, informational tags, bootstrap values, that should be importable into TaxonWorks.
- These imported annotations should be propagated out as tags to everything (every OTU?) that inherits from a node, based on the hierarchy.
- Question: is this going to litter the world with tags everywhere?
- Will these tags be able to be used as characters associated with entities in their own right?
- These imported annotations should be propagated out as tags to everything (every OTU?) that inherits from a node, based on the hierarchy.
- If one created a fully marked-up tree in NeXML that had nodes annotated with, for example, clade names, informational tags, bootstrap values, that should be importable into TaxonWorks.
Implementation plan and milestones
- Proof of concept, all data to be discarded
- Create basic tables
- Import taxonomic hierarchy from Plecoptera Species File
- Develop user interface
- Import taxonomic hierarchy from Embioptera Species File
- Add log on with levels of access and saved user data
- Enable editing
- Handle citations including authors and publication data
- Handle images
- Add anything else required for LepIndex
- Enforce compliance with Code of Zoological Nomenclature
- Handle ecological relationships
- Add anything else required for Universal Chalcidoidea Database
- Import LepIndex
- Import Universal Chalcidoidea Database
- Complete functionality required for existing databases
- Handle specimen data
- Handle character data
- Provide keys
- Tools to assist taxonomic revisions
- Private species files
- Generate text to drop in manuscripts
- Merge private data back into public database
- Verify that all essential data from existing databases can be handled
- Import all existing species file, MX and 3i databases
- Develop data exchange with other applications
- GBIF
- ZooBank
- Global Names Architecture
- New functionality
- Collection data for Illinois Natural History Survey
- Nomenclature codes other than zoological
Links and Resources
- Functional Requirements and Use Cases General paper on formatting and constructing use cases
- Use Cases from NESCent