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PhyloTastic: Names-Based
Phyloinformatic Data Integration
Rutger Vos
Re-use of phylogenetic knowledge
Currently, mostphylogenetic
knowledge is not easily re-used
due to a lack of:
• archiving...
Phylomatic: automated re-use of
phylogenetic knowledge
• In a recent survey of practices of
re-use of phylogenetic knowled...
Phylotastic: generalizing and
modularizing phylomatic-ish functionality

Phylotastic was conceived by NESCent’sHackathons,...
Phylotastic: a design
pattern for phylogenetic
data re-use
1.

Input list of names

2.

Controller queries TNRS
with list ...
Cross-pollinations and spin-offs
TaxoSaurus: the PhyloTastic TNRS
• A simple, asynchronous, RESTful API that
communicates in JSON.
• Modular design: multip...
TaxoSaurus: the PhyloTastic TNRS
/submit - POST or GET a list of scientific names to
the service and retrieve a JSON token...
TaxoSaurus: the PhyloTastic TNRS
/retrieve/<token>- GET the result of a TNRastic query.
• Parameters: none
• Returns: a JS...
TaxoSaurus: the PhyloTastic TNRS
/sources/<source_id>- GET the details about a
particular source, or all sources if no ID ...
TaxoSaurus: the PhyloTastic TNRS
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PhyloTastic: names-based phyloinformatic data integration

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Lightning talk to the 2013 TDWG conference symposium on phyloinformatics, brief report on PhyloTastic with special attention to the taxonomic name reconciliation service TaxoSaurus.

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PhyloTastic: names-based phyloinformatic data integration

  1. 1. PhyloTastic: Names-Based Phyloinformatic Data Integration Rutger Vos
  2. 2. Re-use of phylogenetic knowledge Currently, mostphylogenetic knowledge is not easily re-used due to a lack of: • archiving; • awareness of best practices; • community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a much larger tree.
  3. 3. Phylomatic: automated re-use of phylogenetic knowledge • In a recent survey of practices of re-use of phylogenetic knowledge, Phylomatic was the most frequently used method for obtaining trees, e.g. in studies of phylogenetic community structure. • Phylomatictakes a set of input taxa and extracts them from a reference phylogeny by pruning and grafting. • The reference phylogeny is usually APG-III • Taxon names are matched exactly or grafted on. • Branch lengths are either retained or modeled (bladj)
  4. 4. Phylotastic: generalizing and modularizing phylomatic-ish functionality Phylotastic was conceived by NESCent’sHackathons, Interoperability, Phylogenies (HIP) working group and was initiated by several dozen participants at a NESCent hackathon on June 48, 2012. A second hackathon took place at iPlant’s headquarters in Tucson, Arizona on January 28 through February 1, 2013.
  5. 5. Phylotastic: a design pattern for phylogenetic data re-use 1. Input list of names 2. Controller queries TNRS with list of names 3. TNRS provides token with redirect to results 4. Controller gets TNRS results 5. Controller queries Treestore for trees with TNRS taxa 6. Controller POSTsTreestore matches, GETssubtree back 7. Treestore (or proxy) performs pruning and grafting 8. Annotated subtree is returned
  6. 6. Cross-pollinations and spin-offs
  7. 7. TaxoSaurus: the PhyloTastic TNRS • A simple, asynchronous, RESTful API that communicates in JSON. • Modular design: multiple taxonomies can be ingested and queried • Built around the iPlant TNRS service • Available at taxosaurus.org
  8. 8. TaxoSaurus: the PhyloTastic TNRS /submit - POST or GET a list of scientific names to the service and retrieve a JSON token to access results. Parameters: • query: newline separated list of scientific names. OR • file: a text file containing newline separated scientific names. • source (optional): a comma separated list of taxonomic source ids (see /sources/list). • code (optional): the abbreviation for one of the nomenclature codes (ICZN/ICN/ICNB).
  9. 9. TaxoSaurus: the PhyloTastic TNRS /retrieve/<token>- GET the result of a TNRastic query. • Parameters: none • Returns: a JSON object containing the accepted names /sources/list – GET a ranked list of available sources • Parameters: none • Returns: a JSON object containing the list of source IDs
  10. 10. TaxoSaurus: the PhyloTastic TNRS /sources/<source_id>- GET the details about a particular source, or all sources if no ID specified • Parameters: <source_id> or none • Returns: a JSON object containing the source details /delete/<token>- GET or POST or DELETE. Cancels a running job • Parameters: <token>, the hash of the job to cancel • Returns: a JSON object indicating success or an error
  11. 11. TaxoSaurus: the PhyloTastic TNRS
  12. 12. Voettekst vullen: Invoegen|Koptekst en voettekst / Insert|Header & Footer

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