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Description about the files in the extdata directory

All of the files in the extdata directory, with the exeception of the validation_summary.tsv file, were manually created/edited.

These files are necessary for 1) the bugphyzz package to work properly and 2) a convenient way for curators to update the files.

What follows is the description of each file.

attribute_sources.tsv

Contains the original sources of bugphyzz annotations.

Columns:

Column Description
Attribute_source The abbreviated name of the source. This is the one used in the output of importBugphyzz.
Confidence_in_curation One of three: high, medium, low.
Evidence * The type of evidence supporting the annotations in the original source.
full_source The full name of the source. It could be a citation, a link to webpage or project, etc.

* Evidence Options:

  • exp. Inferred from experiment.
  • igc. Inferred from genomic context.
  • nas. Non-traceable author statement.
  • tas. Traceable author statement.
  • tax. IBD = inferred from biological aspect of descendant.
  • asr. anscestral state reconstruction.

attributes.tsv

It contains the description of the attribute values included in bugphyzz.

Columns:

Column name Description
attribute The name of the attribute.
validity The type of the attribute, either 'logical' for categorical values or 'numeric' for ranges.
ontology Mapping to an ontology term (if possible).
attribute_group The group(s) where an attribute name could be found.
description The meaning of the attribute described in the 'attribute' column.

spreadsheet_custmolinks.tsv

Links for datasets in google spreadsheets that are not in tidy format and need to be converted to tidy format.

Columns:

Column name Description
physiology Name of the physiology or attribute group.
ontology If applicably, mapping to an ontology term.
link Link to the csv export.
functionname The name of the function (unexported) in bugphyzz.
source_link Link to the source spreadsheet on Google Docs.

spreadsheet_links.tsv

Links for datasets in spreadsheets that are already in tidy format.

Columns:

Column name Description
physiology Name of the dataset. Equivalent to attribute group.
ontolgy Mapping to an ontology term if applicable.
sig_type The type of the signature. Either range for numeric or logical for categorical and binary values.
link Link to the csv export.
source_link Link to the source spreadsheet.

curation_template.tsv

Contains the formal description of the data model in the spreadsheets imported by the physiologies funtion.

Columns:

Column name Description
column_name Name of the column in the spreadsheet.
requiredness Whether the column needs to be present in all attributes (required) or not (optional).
required_column_order Order of the column if required.
attribute_types Types of the attributes. Not R classes. Import function behavior will change based on this values.
valid_values A regular expression with the values that are accepted. Except for the column 'Attriubte' which is a function name ('.attributes').
value_test If 'string' the test of validity is based on the regular expresion. If '.attributes', it's based on the function .attriubtes (no exported).
column_class One of the R classes for atomic vectors.

thresholds.tsv

Tresholds for converting numeric/range data to categorical.

Columns:

Column name Description
Attribute_group Physiology. Name of the spreadsheet.
Attribute The actual attribute used.
lower lower threshold.
uppwer upper threshold.
unit units used for numeric data.

validation_summary.tsv

This file was obtained from the waldronlab/taxPProValidtion repository hosted on GitHub. It contains the results of a 10-fold cross-validation analysis of the ancestral state reconstruction (ASR) methods used to get annotations for the package.

Detailed information (code and explanation) can be found on the repository.

The file was downloaded on May 31, 2024 from this URL (pay attention to the commit hash):

https://raw.githubusercontent.com/waldronlab/taxPProValidation/a7a31b0/validation_summary.tsv

The code used, which was executed directly in the extdata directory, was:

This is version 1.0.4

wget https://raw.githubusercontent.com/waldronlab/taxPProValidation/cc45761/validation_summary.tsv
Column name Description
method ASR method (phytools-ltp or castor-ltp)
rank Taxonomic rank (all, genus, species, strain). "all" was used for the output of importBugphyzz.
physiology The name of the attribute group.
attribute The name of the attribute or attribute value.
mcc_mean The mean of Mathew's correlation coefficient for discrete only.
mcc_sd The standard deviation of Matthew's correlation coefficient for discrete only.
r2_mean The mean of the R-squared for numeric only.
r2_sd The standard deviation of the R-squared for numeric only.
ltp_bp Interesction between taxa in bugphyzz (per attribute/attribute value) and the ltp tree.
bp Taxa in bugphyzz (per attribute/attribute value).
ltp_bp_phys Intersection between taxa in bugphyz (per attribute group) and the ltp tree.
bp_phys Total taxa in the bugphyzz (per attribute group).
ltp Number of taxa in the LTP tree.
nsti_mean The mean of the NSTI values. This was calculated for all physiologies, but it's only relevant for numeric ones.
nsti_sd The standard deviation of the NSTI values. This was calculated for all physiologies, but it's only relevant for numeric ones.
ltp_bp_per Intersection of LTP tree and bugphyzz (per attribute/attribute value) in numbers.
ltp_bp_phys_per Intersection of LTP tree and bugphyzz (per physiology/attribute group) in percentage.