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

1. PhyloTastic: Names-Based
Phyloinformatic Data Integration
Rutger Vos

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. 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. 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. 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. Cross-pollinations and spin-offs

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. 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. 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. 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. TaxoSaurus: the PhyloTastic TNRS

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