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MIAPA checklist input form
Other than the initial section and exceptions noted below, this version is a literal, unimproved implementation of the MIAPA draft checklist produced at the workshop of the Phylogenetic Standards group at the 2011 TDWG meeting.   The nature of the requirements is unclear in many cases.  In some cases "must" or "required" is used; in other cases, "should" or "desirable" is used; and in other cases there is merely a descriptive phrase, e.g., invoking "software used" without saying whether this item is required or not.  In every case we have tried to follow the original checklist exactly, including flaws.  

The exceptions and additions are as follows:
* based on the "well described" language in the checklist, we added a question about the nature of the topology as a representation of the method's output
* we have assumed that the topology and character matrix are external resources with a URI
* we have added a new section that includes such things as the annotator, an internal name for this study, and a literature citation
* we have included an "other" box for each question
* we have included a free-text comment with each major section
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Information for the purposes of this study
Metadata for this record, for the purposes of Phylotastic hackathon #2.
annotator *
a local name or identifier for this tree
Publication: author list
comma-separated list of authors
Publication: year
Publication: title
Publication: citation (free text)
Publication: DOI
Other information for the purposes of this study
Location of data resources
A purl.org/phylo URI that resolves to the data resource.
Topology URI
The topology should be "well described", as applicable to the inference method being used. For example, a likelihood for maximum likelihood analysis. For Bayesian analyses this should also include the burn-in period excluded, and the convergence of the chain(s). This may also include more then one topology, for example a sample from the posterior probability distribution for Bayesian, or equally scoring topologies for a maximum parsimony analysis.
Character matrix URI
Other information on the location of data resources
Annotations of the tree as a whole
These are annotations that apply to the whole tree.
Alignment Method: name of software used, version of program
Alignment Method: parameters used (or default if default values were used).
Alignment Method: whether alignment was manually corrected or edited
Clear selection
Tree Inference Method: name of software used, version of program
Tree Inference Method: parameters used, including model of evolution, and optimality criterion
Typically, inference programs provide these in their log files, and thus the information could be copied from there.
Tree Inference Method:  character weights if (normally then morphological) characters were weighted.
Typically, inference programs provide these in their log files, and thus the information could be copied from there.
Topology: nature of topology as representation of inference method
Specify details (e.g., number of trees in consensus) in the "other" section below.  A search is either exhaustive (all possible trees) or non-exhaustive (which is what we mean by "incomplete" below although we could have said it better)
Clear selection
Topology: Is this a gene tree or species tree?
Clear selection
Topology: Is this topology rooted or not?
Clear selection
Other annotations of the tree as a whole
Character matrix: aligned data matrix that is the basis for the tree (by having been the input for the tree inference method)
Character matrix: Data type must be provided, for example DNA, RNA, protein, morphology, etc.
Clear selection
Character matrix: For molecular matrices, the accession numbers (and respective database(s) if different from Genbank) of the sequences used for each row must be provided
Clear selection
Character matrix: a mapping that relates each row identifier to a tip of the topology
Clear selection
Character matrix: a mapping that relates each accession number or specimen identifier to a row label
Clear selection
Other annotations of the character matrix as a whole
OTUs (Operational Taxonomic Units)
All terminal nodes should be appropriately labelled and referenced in one of the following ways. Internal nodes need not be.
OTUs: A meaningful external identifier (a combination of database or resource and identifier/accession within that database).
Where binomials are provided without clear knowledge that these represent external references, indicate "not provided" but note this below under "other comments".
Clear selection
OTUs: For specimens, museum, collection (if applicable), and specimen identifier.
Alternatively, if a specimen is not in a museum collection, use the laboratory, laboratory collection, and accession within that collection
Clear selection
OTUs: Precise (GPS) georeferences for specimens are highly desirable (but not always available).
Clear selection
Other annotations of the OTUs
Branches
[Arlin: note that bootstrap values typically apply to splits in an unrooted tree]
Branch lengths: Some measure of branch length required unless it is not applicable to the analysis method.
Further semantics of the measure should be implied by the tree inference method.  For taxonomic frameworks, branch lengths are not applicable.
Clear selection
Branch support: Some value of branch support should be provided, for example posterior probability, or bootstrap value, unless it is not applicable to the analysis method.
Clear selection
Other annotations of the branches
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