MongoDB models

[NicolasKieffer]

This issue will contain all the information about the data to be stored in mongoDB.

Feel free to add any documentation to enrich the models (structure of the data we store) here.

[NicolasKieffer]

Datasets structure

Currently, a "dataset", a "code", a "lab material" or a "protocol" is stored as a "dataset" in our database. They then "share" the same properties.

I will add all properties from new GUI forms, just tell me if any properties are missing (there is no limit, so we can add an "RRID" property instead of using the existing "DOI" property)

Perhaps we should create a specific structure for each of them (I will at least integrate all possible properties into the existing model).

List of avaiable current properties of "data objects" (datasets, codes, materials or protocols): here

property name	type	description
id	String	id property of the data object
dataInstanceId	String	dataInstance id of the data object (id used in the TEI file)
sentences	List of Sentence*	list of sentences
reuse	Boolean	"reuse" property of the data object
qc	Boolean	"quality control" property
representativeImage	Boolean	"representative image" property
issue	Boolean	"issue" property
notification	String	notification property (store the notification text content)
highlight	Boolean	"highlight" property
cert	String	cert value (between 0 and 1)
dataType	String	datatype of the data object
subType	String	subtype of the data object
description	String	description of the datatype/subtype
bestDataFormatForSharing	String	best data format for sharing of the datatype/subtype
bestPracticeForIndicatingReUseOfExistingData	String	best practice for indicating re-use of existing data of the datatype/subtype
mostSuitableRepositories	String	most suitable repositories of the datatype/subtype
DOI	String	DOI of the data object
name	String	name of the data object
comments	String	comments of the data object
status	String	status of the data object: saved (not valid but saved) OR valid (valid) OR modified (a user modifies it)

Note: a sentence just have two properties: an id and the text

Here are the new forms for "data objects":

Datasets from

Codes form

Materials form

Protocols form

[Souad314]

This excel sheet also describes the inputs in detail on the last tab (Tab 7 - the other tabs are notes on the current html screens)

All Objects

• Suggested Documentation for each object contains repeated fields (Name, etc), [associated excel sheet has coloured cells indicating changes to make it easier]
• Properties are in order of appearance in UI - each property after the "issue" property were left in the table under the assumption they are required in backend storage or other processes
• removed some properties which have no space (highlight, best practice, etc)
• Note that alignment is slightly off, everything is kind of blurry - (apologies) - all added fields should have the same fonts/colours/alignments as existing screens
• Found icon images (stolen from quick Google search) to go with new fields in UI:
• -Key Icon
• -Catalog Icon
• -Microscope Icon
• -Citation Icon

Datasets

Suggested Documentation

property name | type | description | Associated text in UI | Notes -- | -- | -- | -- | -- name | String | name of the data object | "Dataset-x" |   dataType | String | datatype of the data object | Datatype |   subType | String | subtype of the data object | Subtype |   reuse | Boolean | reuse property of the data object | This dataset is re-used from another public or private source |   representativeImage | Boolean | representative image property | This dataset is a Representative Image (or another type of media) |   qc | Boolean | quality control property | This dataset was created for Quality Control (QC) or confirmatory purposes |   DOI | String | DOI of the data object | Stable URL, DOI, or other link to this object |   PID | String | Accession Number or PID of the data object (not an URL), can be "not applicable" | Accession Number/Permanent Identifier (PID) |   comments | String | comments of the data object |   |   issue | Boolean | issue property | There is an issue with the information provided in the manuscript text |   id | String | id property of the data object |   |   dataInstanceId | String | dataInstance id of the data object (id used in the TEI file) |   |   sentences | List of Sentence* | list of sentences |   |   status | String | status of the data object: saved (not valid but saved) OR valid (valid) OR modified (a user modifies it) |   |   notification | String | notification property (store the notification text content) |   |   cert | String | cert value (between 0 and 1) |   |     |   |   |   | *Input fields for datatypes do not change depending on other inputs, i.e. Re-Use datasets have the same language and requirements as New datasets in the UI, Rep images can be re-use, QC, and any other combination

Code and Software

Code: New Custom Script:

Re-Use Custom Script:

Software:

Suggested Documentation

property name | type | description | Associated text in UI | Notes -- | -- | -- | -- | -- name | String | name of the code object |   |   subType | String | subtype of the code object | Subtype |   reuse | Boolean | reuse property of the code object | This item is re-used from a public or private source |   version | String | the version number for the associated software or package | Version |   DOI | String | DOI of the code object | Stable URL, DOI, or other link to this object |   RRID | String | Research Resource Identifier (RRID) associated with software and lab materials, not always available, not an URL | Research Resource Identifier (RRID) |   comments | String | comments of the code object |   |   issue | Boolean | issue property | There is an issue with the information provided in the manuscript text |   id | String | id property of the code object |   |   dataInstanceId | String | dataInstance id of the code object (id used in the TEI file) |   |   sentences | List of Sentence* | list of sentences |   |   status | String | status of the code object: saved (not valid but saved) OR valid (valid) OR modified (a user modifies it) |   |   notification | String | notification property (store the notification text content) |   |   cert | String | cert value (between 0 and 1) |   |   DataType | [always Code and Software on this part of screen] | not a choice for users, when on Code screen, all new added datasets are DataType=Code and Software |   | if Subtype=custom script and Re-use = No, then different inputs displayed, if Subtype=custom script and Re-Use = Yes, then Version removed

Lab Materials

New Material

Material Re-Use

Suggested Documentation

property name | type | description | Associated text in UI | Notes -- | -- | -- | -- | -- name | String | name of the material |   |   subType | String | subtype of the material | Subtype |   reuse | Boolean | reuse property of the material | This item is re-used from a public or private source |   labSource | String | name for source of the material (if re-use) | Source (Name of Lab or Commercial Source) |   Catalog | String | Catalog Number associated with material (asks for Lab Name if Source is Private) | Catalog Number |   RRID | String | Research Resource Identifier (RRID) associated with software and lab materials, not always available, not an URL | Research Resource Identifier (RRID) |   comments | String | comments of the data object |   |   issue | Boolean | issue property | There is an issue with the information provided in the manuscript text |   id | String | id property of the code object |   |   dataInstanceId | String | dataInstance id of the code object (id used in the TEI file) |   |   sentences | List of Sentence* | list of sentences |   |   status | String | status of the code object: saved (not valid but saved) OR valid (valid) OR modified (a user modifies it) |   |   notification | String | notification property (store the notification text content) |   |   cert | String | cert value (between 0 and 1) |   |   DataType | [always Lab Materials on this part of the screen] | not a choice for users, when on Materials screen, all new added datasets are DataType=Lab Materials |   | if re-use is no, there are less inputs, if yes then two source inputs (2nd screenshot)

Protocols

New Protocol Re-Use - Another Protocol (is the "Private" source)

Re-Use - Manufacturer's Instructions (is the "Public" source)

Suggested Documentation

property name | type | description | Associated text in UI | Notes -- | -- | -- | -- | -- name | String | name of the protocol object |   |   reuse | Boolean | reuse property of the protocol object | This item is re-used from a public or private source |   protocolSource | Boolean | choice for if yes object is a re-use protocol (methods section) is Manufacturer's Instructions or another protocol | Protocol Type [Choices: 1-"Another Protocol"; 2-"Manufacturer's Instructions"] | See Screenshot 2 and 3 DOI | String | DOI of the data object | Stable URL, DOI, or other link to this object |   comments | String | comments of the data object |   |   issue | Boolean | issue property | There is an issue with the information provided in the manuscript text |   id | String | id property of the code object |   |   dataInstanceId | String | dataInstance id of the code object (id used in the TEI file) |   |   sentences | List of Sentence* | list of sentences |   |   status | String | status of the code object: saved (not valid but saved) OR valid (valid) OR modified (a user modifies it) |   |   notification | String | notification property (store the notification text content) |   |   cert | String | cert value (between 0 and 1) |   |   DataType | [always Other on this part of the screen] | not a choice for users, when on Protocols screen, all new added datasets are DataType=Other -Note: if re-use is yes and type is Manufacturer's Instructions, no further inputs required for object (2nd screenshot) |   |   subType | [always Protocol on this part of the screen] | not a choice for users, when on Protocols screen, all new added datasets are subType=Protocol |   |  

[Souad314]

@NicolasKieffer Here are some proposed changes to Protocols: During the 11-Mar Tech Meeting (of epic length), we talked about adding Protocol as the Datatype for the ability to have Published Protocol and Manufacturer Instructions as Subtypes. So, after much consideration, here are some notes for implementation:

1. Wiki

• I have added these pathways to the Wiki Protocol Protocol: Published Protocol Protocol: Manufacturer Instructions

Question: Datatypes are ready to be refreshed, does this affect already curated documents - do their tokens need to be refreshed, and does that affect OCR docs?

2. Report

• Changed this report (with all possible pathways - 2nd Tab, Protocol Section only) ASAP Template 18 Feb to include the output pathways associated with this change
• • Although re-use is still an input on the report tab (at the moment), the functionality is erased when Protocol subtypes exist: To further explain,
• When no subtype selected (Subtype=none), Protocol is "New"
• If any other subtype is selected (Subtype=Published Protocol; Subtype=Manufacturer Instructions), this Protocol is considered re-use
• If Manufacturer Instructions selected, Dataset is considered Done (Shared/Cited)
• Summary Tab numbers to reflect new inputs
• DS UI version of article not yet up to date

3. Burger Screens

• Changes made to Protocol Screens
• Changes to suggested Documentation: (formatted for better visualization in doc)
• No longer need "ProtocolSource" input
• Re-Use not available for this datatype

property name | type | description | Associated text in UI | Notes -- | -- | -- | -- | -- name | String | name of the protocol object |   |   subType | String | "Protocol Type" in Desired ScreensSubtype = None: - New Protocol (Desired Screen 1)Subtype = Published Protocol (Desired Screen 2)Subtype = Manufacturer Instructions (Desired Screen 3) |   |   reuse | Boolean | reuse property of the protocol object | This item is re-used from a public or private source | No Re-Use available because Subtypes (Published Protocol and Manufacturer Instructions imply re-use already, so this field should not be changeable under these subtype conditions) protocolSource | Boolean | choice for if yes object is a re-use protocol (methods section) is Manufacturer's Instructions or another protocol | Protocol Type [Choices: 1-"Another Protocol"; 2-"Manufacturer's Instructions"] |   DOI | String | DOI of the data object | Stable URL, DOI, or other link to this object |   comments | String | comments of the data object |   |   issue | Boolean | issue property | There is an issue with the information provided in the manuscript text |   id | String | id property of the code object |   |   dataInstanceId | String | dataInstance id of the code object (id used in the TEI file) |   |   sentences | List of Sentence* | list of sentences |   |   status | String | status of the code object: saved (not valid but saved) OR valid (valid) OR modified (a user modifies it) |   |   notification | String | notification property (store the notification text content) |   |   cert | String | cert value (between 0 and 1) |   |   DataType | [always Protocol on this part of the screen] | not a choice for users, when on Protocols screen, all new added datasets are DataType=Protocol (or DataType Other) |   |  

New Protocol (Datatype=Protocol, Subtype=None)

Published Protocol (Datatype=Protocol, Subtype=Published Protocol)

Manufacturer Instructions (Datatype=Protocol, Subtype=Manufacturer Instructions)

[NicolasKieffer]

Datatypes are ready to be refreshed, does this affect already curated documents - do their tokens need to be refreshed, and does that affect OCR docs?

This will not affect the document, only the "select" elements (selectable lists of data types/subtypes). Datasets using "old" datatype/subtype will still have the old datatype/subtype values