Advancing MIAPA - Revision history

Hilmar: Hilmar moved page AdvancingMIAPA to Advancing MIAPA

2013-02-03T00:32:46Z

Hilmar moved page AdvancingMIAPA to Advancing MIAPA

← Older revision	Revision as of 00:32, 3 February 2013
(No difference)

Hilmar: /* Lessons learned from tree-finding and annotation */

2013-02-03T00:31:16Z

Lessons learned from tree-finding and annotation

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 #* imagine that you have to publish an analysis using a phylogenetic tree-- how do you describe it?  "The phylogeny of 40 mammal species was obtained via phylotastic (phylotastic.org
 #* citation information
 == Lessons learned from tree-finding and annotation ==

Hilmar: /* MIAPA Resources */

2013-02-03T00:28:52Z

MIAPA Resources

← Older revision		Revision as of 00:28, 3 February 2013
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	** Emily McTavish's [https://docs.google.com/a/utexas.edu/spreadsheet/ccc?key=0Av6YLPeop2n0dGZiMjNGS2NleWNvQlVSeThVQXdSdmc#gid=0 Tree Annotation Vocabulary] as resulting from the [[Phylotastic I]] hackathon. Includes a mapping to MIAPA draft checklist attributes.		** Emily McTavish's [https://docs.google.com/a/utexas.edu/spreadsheet/ccc?key=0Av6YLPeop2n0dGZiMjNGS2NleWNvQlVSeThVQXdSdmc#gid=0 Tree Annotation Vocabulary] as resulting from the [[Phylotastic I]] hackathon. Includes a mapping to MIAPA draft checklist attributes.
	** [http://www.slideshare.net/ElliottHauser/phylogenetics-data-provenance-survey-results Slideshow] with some results from the [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey MIAPA community survey] orchestrated by the Open Tree of Life project in fall 2012.		** [http://www.slideshare.net/ElliottHauser/phylogenetics-data-provenance-survey-results Slideshow] with some results from the [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey MIAPA community survey] orchestrated by the Open Tree of Life project in fall 2012.
			* Development:
			** [http://github.com/miapa/miapa MIAPA repo on Github]
	* Ontologies		* Ontologies
	** [http://bioportal.bioontology.org/ontologies/49276?p=terms phylont] from [http://arnetminer.org/publication/phylont-a-domain-specific-ontology-for-phylogeny-analysis-3601839.html;jsessionid=E93A88FA38E826E1113A957BBA5BB352.tt Maryam Panahiazar, et al]
	** [http://www.evolutionaryontology.org/cdao CDAO]		** [http://www.evolutionaryontology.org/cdao CDAO]
	* ~~Development~~:		** [http://www.w3.org/TR/prov-o/ W3C Provenance Ontology]
	** [http://~~github~~.com/~~miapa~~/~~miapa MIAPA repo on Github~~]		** [http://code.google.com/p/information-artifact-ontology/ Information Artefact Ontology]
	** ~~Template development after~~ the [~~https~~://~~github~~.~~com~~/~~phylotastic~~/~~treestore~~/~~tree~~/~~master~~/terms ~~TNRS~~ ontology] ~~developed at~~ (~~and after~~) ~~Phylotastic I.~~		** [http://theswo.sourceforge.net/ Software Ontology] (includes the [http://edamontology.org/ EDAM ontologies])
			** [http://bioportal.bioontology.org/ontologies/49276?p=terms phylont] from [http://arnetminer.org/publication/phylont-a-domain-specific-ontology-for-phylogeny-analysis-3601839.html;jsessionid=E93A88FA38E826E1113A957BBA5BB352.tt Maryam Panahiazar, et al]. (We did not use this.)

	== Annotation ==		== Annotation ==

Hilmar: /* Lessons learned from tree-finding and annotation */

2013-02-03T00:19:22Z

Lessons learned from tree-finding and annotation

← Older revision		Revision as of 00:19, 3 February 2013
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	#* citation information		#* citation information

	=== Lessons learned from tree-finding and annotation ===		== Lessons learned from tree-finding and annotation ==

	* data frequently is not readily accessible online		* data frequently is not readily accessible online
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	* OTUs checklist question may be redundant: why have external identifier and then ask for collections information?		* OTUs checklist question may be redundant: why have external identifier and then ask for collections information?
	* OTU external refs in checklist: not applicable for supertree methods, consensus methods, hand-crafted		* OTU external refs in checklist: not applicable for supertree methods, consensus methods, hand-crafted


	== MIAPA Resources ==		== MIAPA Resources ==

Hilmar at 00:19, 3 February 2013

2013-02-03T00:19:04Z

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	=== Factors shaping our conception of source-tree annotations ===		== Factors shaping our conception of source-tree annotations ==

	# what folks in the evoinfo community believe is the Minimal Information About a Phylogenetic Analysis (MIAPA)		# what folks in the evoinfo community believe is the Minimal Information About a Phylogenetic Analysis (MIAPA)

Hilmar: /* MIAPA */

2013-01-31T23:03:34Z

MIAPA

New page

=== Factors shaping our conception of source-tree annotations ===

# what folks in the evoinfo community believe is the Minimal Information About a Phylogenetic Analysis (MIAPA)
#* The current synopsis of this is the MIAPA checklist from teh 2011 TDWG meeting.
# need to support assignment of credit (blame) for tree-producers and phylotastic service-providers
# need to support licensing that protects creators, resource-providers and end-users
# need to contribute to a credible provenance report for phylotastic-generated trees
#* e.g., a tree might be returned with information as follows (free text form): "This tree was obtained on Jan 29, 2013. An input list of 58 names was submitted to Taxosaurus, resulting in 45 valid species binomials ( list ). This list was sent to a pruner with instructions to prune out the indicated species from the phylogeny of Bininda-Emonds, et al. 2007. The resulting sub-tree with 40 species was scaled using teh DateLife service. "
# support the most common user criteria for phylotastic searching
#* limits on source trees
#** '''return tree with maximal coverage of list ::= { species }'''
#*** specify namespace of <list>
#** restrict by publication status (published or not)
#** restrict by publication year (e.g., no trees older than 5 years)
#** restrict by author (e.g., author = bininda-emonds)
#** restrict by other citation information (e.g., jrnl = index fungorum)
#** restrict by method
#*** '''use (exclude) trees made with method class = { parsimony, likelihood, Bayesian, distance, supertree, supermatrix, hand-crafted. . . } '''
#*** use (exclude) trees made with evolutionary model = { }
#*** '''use (exclude) trees made with software = { RaXML, BEAST, PAUP*, . . . }'''
#*** other restrictions (e.g., supertree, . . . )
#** restrict by availability of source data such as character matrix
#*** restrict by minimum number of characters in matrix
#** '''restrict by type of source data = { molecular, morphological, mixed } '''
#** restrict by annotation level = { platinum, gold, silver, bronze, polystyrene }
#** require feature
#*** '''require support values'''
#*** require rooting
#*** '''require branch lengths'''
#*** require fully resolved
#*** require other features
#* limits on phylotastic manipulations
#** disallow species substitution
#** disallow grafting of source trees
#** scaling: provide median age estimates
#** scaling: provide only lower age estimates
#** TNRS: prohibit fuzzy matching
#** TNRS: use matches from source = { NCBI, ITIS, et }
# support adequate annotation of the provenance of the resulting phylotastic tree
#* imagine that you have to publish an analysis using a phylogenetic tree-- how do you describe it? "The phylogeny of 40 mammal species was obtained via phylotastic (phylotastic.org
#* citation information

=== Lessons learned from tree-finding and annotation ===

* data frequently is not readily accessible online
** e.g. Jetz one must go to birdtree.org
** e.g., we obtained hymenoptera tree by pers. communication from Peters
** only one of the studies has trees in TreeBASE (GEBA)
** another study has a tree in Dryad (Smith)
* authors often don't provide minimal information explicitly
** whether or not a tree is rooted is usually not explicit
*** e.g., taxonomic hierarchies (APG, ToLWeb, NCBI) imply rootedness
*** e.g., Peters, et al 2011 never invokes the term "root" but we infer rooting from the description of outgroups not present in the final tree
** the methodology is largely unexplained for curated or hand-crafted taxonomic frameworks like APGIII or NCBI
* a study frequently has several trees by slightly different methods, but the checklist seems to imply one method
** e.g., Goloboff molecules only vs. molecules with morphology
** e.g., Bininda-Emonds best dates vs min dates vs max dates
* sometimes a study has many trees that all represent outputs of the same method
** e.g., Jetz provide a large sample from the posterior distribution
* process of constructing tree does not follow sequences--> alignment--> tree
** e.g., supertree method in Bininda-Emonds
** e.g., hand-crafted APG, Smith, trees
* process of constructing tree cannot be condensed easily
** e.g., Goloboff, iterative procedure with divide-and-conquer search to find parsimony tree ("tree fuse" & "sector" search repeated)
** GEBA tree, { missing explanation }
** partitioned alignment (e.g., Smith, et al), but miapa implies "model of evolution" as though there were only one, whereas in Peters, et al there are 2 models for 2 partitions
* clustering to define orthologs not included in checklist, but seems important
** Smith phlawd, alignment: no pre-orthology.
* mixed data is common
** Goloboff has morpho and molecular
** multiple studies have DNA (e.g., SSU rDNA) and protein sequences
* concatenated alignments are common, e.g., multiple proteins
** this means accession:OTU mapping is not 1:1 but many to one
* not encountered in our inputs but sometimes the OTU is <genus_sp> and the data are fused from multiple species (this is common in MorphoBank)
* many important trees do not have branch lengths
** e.g., APGIII is a taxonomic framework
** e.g., some supertrees don't have branch lengths
* do binomials count as meaningful external identifiers for OTUs?
** in some cases, the methods make clear that these come from a specific source
*** e.g., Goloboff names clearly come directly from NCBI via their bioinfo pipeline
*** e.g., Bininda-Emonds publication declares that naming authority is Wilson & Roeder (Mammal Species of the World)
*** e.g., NCBI taxonomy comes as a database dump wth taxids and synonyms, so it represents its own authority
** usually the naming authority is not clear
* was any study straightforward?
* OTUs checklist question may be redundant: why have external identifier and then ask for collections information?
* OTU external refs in checklist: not applicable for supertree methods, consensus methods, hand-crafted

== MIAPA Resources ==
* The main [[MIAPA]] page. Primarily:
** [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Reconciled_draft_checklist MIAPA draft checklist] from TDWG 2011 workshop.
** Emily McTavish's [https://docs.google.com/a/utexas.edu/spreadsheet/ccc?key=0Av6YLPeop2n0dGZiMjNGS2NleWNvQlVSeThVQXdSdmc#gid=0 Tree Annotation Vocabulary] as resulting from the [[Phylotastic I]] hackathon. Includes a mapping to MIAPA draft checklist attributes.
** [http://www.slideshare.net/ElliottHauser/phylogenetics-data-provenance-survey-results Slideshow] with some results from the [http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey MIAPA community survey] orchestrated by the Open Tree of Life project in fall 2012.
* Ontologies
** [http://bioportal.bioontology.org/ontologies/49276?p=terms phylont] from [http://arnetminer.org/publication/phylont-a-domain-specific-ontology-for-phylogeny-analysis-3601839.html;jsessionid=E93A88FA38E826E1113A957BBA5BB352.tt Maryam Panahiazar, et al]
** [http://www.evolutionaryontology.org/cdao CDAO]
* Development:
** [http://github.com/miapa/miapa MIAPA repo on Github]
** Template development after the [https://github.com/phylotastic/treestore/tree/master/terms TNRS ontology] developed at (and after) Phylotastic I.

== Annotation ==
* representation of metadata: [http://www.nexml.org NeXML]
* some stuff that Rutger did mapping the metadata from ToLWeb XML format onto semantic annotations in NeXML.
** ToLWeb XML described here: http://tolweb.org/tree/home.pages/downloadtree.html
** a simple script that does the conversion: https://github.com/ncbnaturalis/bio-phylo/blob/master/experimental/tolconvert.pl
** Here's an example input file: https://raw.github.com/ncbnaturalis/bio-phylo/master/experimental/tol.xml
** Here's the resulting output file (indented): https://raw.github.com/ncbnaturalis/bio-phylo/master/experimental/tol-nexml-pp.xml