Document toolbox

Tools Schema

Owned by Anna Greenwood (Unlicensed)

Last updated: Jun 20, 2019

1 min read

Some of these fields have Synapse annotations defined: https://github.com/Sage-Bionetworks/synapseAnnotations/blob/master/synapseAnnotations/data/tool.json

Field Name	Description	Synonyms	Column Type	Facet (Y/N)	Required (Y/N)	Destination	Notes	Applies to Which Tool Type
toolName		name, methodName	string	N	Y	link	name is a clickable link, URL sourced from "link" column	computational, experimental, clinical
description		summary	large text	N	Y			computational, experimental, clinical
link	link to access the tool	link	URL	N	Y			computational, experimental, clinical
consortium	Key for mapping	organization, program, fundingAgency	string	Y	N			computational, experimental, clinical
grant	Key for mapping	project	string	Y	N			computational, experimental, clinical
study	Key for mapping		string	Y	N			computational, experimental, clinical
contributor	contributor name	contact	string	N	N			computational, experimental, clinical
contributorContact	synID or email address		entity? email?	N	N			computational, experimental, clinical
toolType	e.g. bench science/experimental, computational, or clinical		string	Y	N		also associated with different icons?	computational, experimental, clinical
subType	mouse model, cell line, R shiny tool, etc		string	Y	N		***is this needed?
reagentType	mouse model, cell line, viral vector		string	Y	N			experimental
softwareType	type of Software, e.g. script, packageLibrary, container, graphical user interface, web user interface, web application		string	Y	N			computational
softwareLanguage	software language e.g. R, python, matlab		string	Y	N			computational
inputDataType	source data for tool e.g. geneExpression, proteomics		string	Y	N			computational
outputDataType	output data of tool e.g. genomicVariants, image, proteomics		string	Y	N			computational
diagnosis	e.g. Late onset AD, Familial AD	tumor type	string	Y	N			computational, experimental, clinical
modelType	e.g. APP mouse model, Trem2 model		string	Y	N			experimental
outputDatasets	datasets generated using this tool or about this tool		entity	N	N		is this data using the tool or about the tool? ie rnaseq data from a workflow tool vs rnaseq data ON a mouse model	computational, experimental, clinical
publications	list of publications?		large text	N	N		what is the expected display and behavior?	computational, experimental, clinical
controlledAccess			boolean	N	N			computational, experimental, clinical
documentation	link to wiki or PDF containing documentation, possibly in Synapse		URL	N	N			computational, experimental, clinical
featured			boolean	N	N			computational, experimental, clinical