DINA User Guide

In-place, in-context verbatim, character-by-character representations of one or more person and/or one or more organization. Example: "M. et Mme Jacques Brossard" as Verbatim Collector in a Collecting Event.

Names of any geographical or topographical feature of public or historical interest. A geographical name is a proper noun applied to a natural, man-made or cultural feature on Earth. A feature can have different names in one or several languages and the names may be provided, together with appropriate information on the feature, in different products like maps and gazetteers as well as respective services. Based on defintion from EU INSPIRE.

Georeferencing means to associate an object with a position in physical space. Postion is most commonly represented using a coordinate reference system, which in turn can be related to a geodetic reference system such as WGS-84.

A definitive, canonical representation of a human in the Agent module that has been ideally disambiguated through inclusion of an externally referenced identifier.

Reverse geocoding is the process of converting a location as described by geographic coordinates (latitude, longitude) to a human-readable place name.

Groups are used to define set of users for administration purpose (mostly permissions). They usually align with collections. A user can belong to more than 1 group.

Groups are also used to defined who owns an object. For example, an object in the object-store always belongs to a group. Objects can only have 1 owner.

With the exception of Administrator, roles are always assigned per group.

Permissions in DINA are strictly related to roles per the table below:

Technicals: Permissions are mostly Role-based access control combined with Discretionary access control with owner.

Users (when explicitly allowed) can access the system. What a user can and cannot do is based on the group(s)/permission(s). When using an external Identity Provider (e.g. ESAS) the user account must be linked to the Identity Provider account. Once done, the user will be able to use a third-party authentication (e.g. ESAS) to access the system.

DINA has some fields that are prefixed with the word "verbatim". Verbatim is defined as "in exactly the same words as were used originally". These fields are used to capture the data as originally represented for example on a label or in in expedition notes.

All object in DINA are identified with UUID (universally unique identifier). While this type of identifier is not considered human-readable (123e4567-e89b-12d3-a456-426614174000) it has the property to be virtually universally unique (chances of duplicates are close enough to zero to be considered negligible). Objects can be uniquely identifed even outside the DINA system.

Machine readable code output that would be obtained from a scanning gun. Can be used as another means of searching the database.

In the context of DINA, date/time can organized in 4 categories:

Form templates are used to customize the user interface by allowing you to choose field visibility and default values. The user can then use them for data entry on a single page or through a split operation.

Field extensions are fields with specific definitions that are defined by known standards. In order to add a specific field extension, a system administrator needs to provide a configuration file to the application.

Managed attributes are attributes that can be created and used by the users on-demand. They are usually used to track data that is not common enough to be captured in a regular field. A managed attribute can be of type integer, string, date or boolean.

Attachments refer to Object Store Component.

Mechanism used to group material samples according to a generic, administrative theme. Should not be confused with Project. Examples might include specimen books or exsiccatae in herbaria where there is a title and a description and possibly enhanced with Managed Attributes for additional metadata that depicts the group’s identity.

A Collection represents the top entity that can contain material-sample. Top collections (or parent collections) generally represent a natural history collection or a laboratory. A collection can contain multiple sub-collection(s).

Darwin Core defines "event" as : An action that occurs at some location during some time. (from DarwinCore). In a Collection Event, the action is the extraction from nature.

Determinations are attached to an Organism. There is always a primary determination defined. Determination history is preserved.

Material Sample represents the main unit of work in DINA. It can be described as: A physical result of a sampling(or subsampling) event.

The material sample can be collected, cultivated, extracted and either preserved or destructively processed.

The concept encompasses the terms materialSample and materialSampleEntity from DarwinCore.

Preparation can either be for preservation or propagation purpose.

A particular organism or defined group of organisms considered to be taxonomically homogeneous. (from DarwinCore). Optionally, it is possible to define a target organism within a material sample.

Project has a start and an end date. It usually links to the organizational definition of project where an objective, a scope, resources and deliverable are defined. A material sample can be linked to multiple projects.

Predefined written procedural method in the design and implementation of experiments in natural sciences. (from Wikidata)

The concept of a split represents the action of creating new material sample(s) from an existing material sample. The provenance of the new material sample(s) is preserved. For example, the action can be a dissection or fungal/bacterial propagation.

Split can be configured using a form template with a Split Configuration setup.

Limitation: The result of a split (called children) cannot have their own collecting event. Since the extraction from nature happened on the first material sample, children will inherit the one from the first parent.

Restriction levels are regulations set by the Public Health Agency of Canada (PHAC) and the Canadian Food Inspection Agency (CFIA). Levels set, or restrictions remarks made will tag the material sample with the appropriate level or note. The “Restricted” button toggle is decoupled from the tags.

Risk groups(RG) are classifications defined by the PHAC based on a biologic’s inherent characteristics and its prevalence for pathogenicity, virulence, risk of spread and availability of effective treatment. The risk group directs the appropriate containment level required to safely handle the specimen and dictates standard operating procedures.

Notes made in the Restrictions Remarks section will have its own red alert box when viewing the material sample. Note that only a single box will be created for the restrictions remarks; a new line does not create a new box.

Only for reporting and record keeping purposes. No alerts will be triggered automatically on assigned date. Multiple actions can exist.

Generic classification description for a storage object that is created. Used as a means of categorizing. A storage unit type can have the grid option meaning that it can store content using coordinates.

Individual instance of a Storage Unit Type. For example, "Room 101" is a storage unit that has a storage unit type of Room.

Data about an object stored or represented in the object-store.

Represents a derivative from a metadata object. Its lifecycle is directly attached to the metadata object meaning that if the metadata object is deleted the derivative will automatically be deleted. Derivatives are usualy a visual representation of the main object when the main object can’t be easily represented like raw formats. They are also used to store thumbnails.

Represents a file uploaded to the object-store-api. The files are uniquely identified and available to attach metadata or derivative.

External resources are represented in the object-store by a URL. No copy or storage of the file is available in the object-store but instead a link to the resource. This is mostly used to allow the object-store to point to a resource that could not be represented as a file (e.g. protocols.io) or that the level of protection required is higher than what the object-store can support.

Information about Primers used for gene amplification of a targeted organism.

Used to track different amplification cycles and melting temperature programmed for each gene region and its associated primer pairs.

Details of the PCR Master Mix used for gene amplification. PCRBatch will connect to Gene Region, PCR Primers and Thermocycler Profiles.

Relationships in Workbooks are expressed as textual representation unless a UUID (Universal Unique Identifier) is provided. The Workbook Upload will need to map the textual representation to existing concepts in the DINA system. With the exception of collecting-event, all records where the relationships are pointing must already exist before the import.

The IN operator can be used to run a query that would return all the elements from a comma separated list.

The previous query would return all records with primaryID is equal to REC-1, REC-2 or REC-4.

The BETWEEN operator can be used to run a query that would return all the elements that are within the upper and lower bound.

The operator is also available on some alphanumeric fields (when configured).

The previous query would return all records where the primaryID is greater or equals to REC-1 and less or equals to REC-9.

This section explains the special characters you can use to refine your searches within the Global Search feature. These options allow you to construct more precise and targeted global searches, helping you find the information you need more effectively.

Operators:

Phrases and Wildcards:

Precedence and Grouping:

Advanced Options:

Escaping Characters:

If you want to use any of the special characters listed above literally in your search query (e.g., searching for + itself), you can escape them with a backslash (\) before the character.