2. Viewing and Downloading the Information

2.1 Viewing the Information

There are various types of records on SynBioHub. They’ve been divided into the following sub-categories:

2.1.1 Viewing a Record

This section consists of a general description of all record pages i.e, this is what a general record page looks like. Additional sections (if any), are further explained in the further sections, under the respective record types. Once you’ve successfully navigated to the record’s home page, you’ll be able to view the parameters in this order:

  • Name: Represents the name of that particular record.

  • ID and version: The next line represents the ID and the version of that record. Every record has a specific ID associated with it and a version which represents the number of times; it has been modified.

  • Type: This specifies the category of biochemical or physical entity. For example DNA, protein, or small molecule that a ComponentDefinition object abstracts for the purpose of engineering design.

  • Generated from: Represents the source from where that record had been generated from.

  • Then, we’ve got five clickable options, that are:

  • Then we have the details of that record. This consists of the following:

    • Type: This specifies the category of biochemical or physical entity. For example DNA, protein, or small molecule that a ComponentDefinition object abstracts for the purpose of engineering design.

    • Role: Clarifies the potential function of an entity in a biochemical or physical context. When it is used for ComponentDefinitions, it MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition.

    • Sequence: The purpose of the Sequence class is to represent the primary structure of a ComponentDefinition object and the manner in which it is encoded. This representation is accomplished by means of the elements property and encoding property.

    • Also, you can view reference as well as citations.

  • Then, we have the section named, other properties. This consists of the following attributes:

    • Ontology for Biomedical Investigations(OBI): A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles.

    • SynBioHub#Owned_by: Username of the design owner.

    • SynBioHub#TopLevel

  • Subsequently, we have the section titled as, Member of these collections. This section contains the list of collection’s to which that particular resource belongs to.

  • Then, we have the attachments page. In this section, you can view the various attachments, of a resource.

  • Additional information may be rendered for a record via visualization plugins.

  • Then, we have a section, titled Member of these collection, which displays the collection, of which that particular record is a part of.

2.1.2 Viewing a Collection

Collection, basically groups together a set of TopLevel objects that have something in common.

On a collection’s home page, other than the details mentioned in the general section, you’ll be able to view a section titled, members. This sections basically contains, the list of records that is included in this particular section. A general description of this section is as follows:

  • Filtering the Table: The first parameter in this section is of filtering the table of contents. This is basically a dropdown menu, which contains various parameters base upon which the table of contents can be filtered. It contains various options such as showing all objects, showing only root objects, biopic:complex, etc.. You may select the option of your choice, from this dropdown menu and then click on filter. This will filter the table and display only those contents which’er as per the parameter that you have selected.

  • Number of Entries: This is also a dropdown menu, which contains certain integer strings. The number of records you want to be displayed on a single page, can be controlled by this option. So, you can choose the value as per your own convenience, which in turn shall display that many records on a single page.

  • Search: By using this search option, you can search for the records of your own choice, just by providing its name. Therefore, for searching a record contained in the table, you need to provide its exact name string.

  • Table: Then we have is the table of contents. It contains the records that are in that very particular collection. This is a sortable table and can be sorted on the basis of multiple parameters ranging from identifier, type or description.

The header of the table as explained as follows:

Table Header Description
Name This contains the name of each and every record that is in that collection, that is provided by the user who had submitted that particular record. Just besides the header there is small figure, clicking on which shall sort this table on the basis of reverse priority of alphabets i.e, Z-A
Identifier This contains the ID or the identifier of that particular record,that is provided by the user who had submitted that particular record. ust besides the header there is small figure, clicking on which shall sort this table on the basis of reverse priority of alphabets i.e, Z-A
Type This represents the type of the record, i.e. whether it is a module, sequence, activity, etc.
Description This is a brief description, that is provided by the user, who’d submitted that particular records. This description, in brief describes, what that particular record does.

2.1.3 Viewing a Module (Definition)

A Module, basically represents a grouping of structural and functional entities in a biological design. Once you’ve successfully navigated to the Module’s home page, other than the parameters described in the general section, you’ll be able to view a few other the parameters, as follows:

  • Type: The record type, as is obvious will be displayed as Module. A Module, basically represents a grouping of structural and functional entities in a biological design.

Just below the clickable options, the VisBol navigator is located, which displays the structure of that particular module. VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL Navigator also has zooming capabilities. This, graphically represents the structure of the module. By hovering your pointer over this structure, you can view the following attributes of that particular module i.e, type of resource, identifier, name and role of the module.

Then, what we have is the section titled, functional components. A FunctionalComponent is an instance of a ComponentDefinition being used as part of a ModuleDefinition. The ModuleDefinition describes how the that describes how the FunctionalComponent interacts with others and summarizes their aggregate function. The parameters included in this section are described in the table below:

Parameter Name Description
Access/Direction 1) Access: The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo on another ComponentInstance or Module contained by a different parent ComponentDefinition or ModuleDefinition (one that does not contain this ComponentInstance). 2) Direction:Each FunctionalComponent MUST specify via the direction property whether it serves as an input, output, both, or neither for its parent ModuleDefinition object.
Definition and MapsTo 1) Definition: The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. ComponentDefinition effectively provides information about the types and roles of the ComponentInstance. 2) MapsTo: When ComponentDefinition and ModuleDefinition objects are composed into structural and functional hierarchies using ComponentInstance and Module objects, it is often the case that some ComponentInstance objects are intended to represent the same entity in the overall design. The purpose of the MapsTo class is to make these identity relationships clear and explicit. For example, consider a ModuleDefinition for a genetic inverter that includes a FunctionalComponent for an abstract repressor protein. When this ModuleDefinition is instantiated within a “higher level” ModuleDefinition that includes a FunctionalComponent for a LacI protein, the MapsTo object can be used to indicate that the repressor protein in the first ModuleDefinition is LacI in the context of the composite design.
Public and Inout 1) Public: Indicates that a ComponentInstance MAY be referred to by remote MapsTo objects. 2) Inout: Indicates that the FunctionalComponent is both an input and output.

Subsequently, just below the functional components we have the Interactions section. Interaction basically, provides a more detailed description of how the FunctionalComponent objects of a ModuleDefinition are intended to work together. It has a table consisting of the following attributes:

Name Description
Interaction/Participation 1) Interaction: Provides more detailed description of how the FunctionalComponent objects of a ModuleDefinition are intended to work together. 2) Participation: Each Participation represents how a particular FunctionalComponent behaves in its parent Interaction.
Participant Definition The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance.
Type/Role 1) Type: Specifies the category of biochemical or physical entity. For example DNA, protein, or small molecule that a ComponentDefinition object abstracts for the purpose of engineering design. For DNA or RNA entities, additional types fields are used to describe nucleic acid topology (circular / linear) and strandedness (double- or single-stranded). 2) Role: Clarifies the potential function of an entity in a biochemical or physical context. When it is used for ComponentDefinitions, it MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO). It may be a product, genetic production, template, etc.

2.1.4 Viewing a Component (Definition)

Component (Definition) is used to represent biological design components such as DNA, RNA and small molecules. Once you’ve successfully navigated to the component’s home page, other than the parameters described in the general section, you’ll be able to view a few other parameters, which are described below.

Just below the details table, you’ll be able to view a table titled, components, which has the following parameters:

Name Description
Access The access property is a REQUIRED URI that indicates whether the ComponentInstance can be referred to remotely by a MapsTo on another ComponentInstance or Module contained by a different parent ComponentDefinition or ModuleDefinition (one that does not contain this ComponentInstance)
Instance The ComponentInstance abstract class is inherited by SBOL classes that represent the usage or occurrence of a ComponentDefinition within a larger design (that is, another ComponentDefinition or ModuleDefinition).
Definition The definition property is a REQUIRED URI that refers to the ComponentDefinition of the ComponentInstance. As described in the previous section, this ComponentDefinition effectively provides information about the types and roles of the ComponentInstance.

Below the components table is another table titled, sequence annotations, having the following attributes:

Name Description
Sequence Annotations The SequenceAnnotation class describes one or more regions of interest on the Sequence objects referred to by its parent ComponentDefinition. In addition, SequenceAnnotation objects can describe the substructure of their parent ComponentDefinition through association with the Component objects contained by this ComponentDefinition.
Location Extended by the Range, Cut, and GenericLocation classes.
Components/Role 1) Components: The components property is OPTIONAL and MAY specify a set of Component objects that are contained by the ComponentDefinition. The set of relations between Component and ComponentDefinition objects is strictly acyclic. 2) Role: Clarifies the potential function of an entity in a biochemical or physical context. When it is used for ComponentDefinitions, it MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO).

2.1.5 Viewing a Sequence

The purpose of the Sequence class is to represent the primary structure of a ComponentDefinition object and the manner in which it is encoded. This representation is accomplished by means of the elements property and encoding property. Once you’ve successfully navigated to the sequence’s home page, other than the parameters described in the general section, you’ll be able to view a few other parameters, which are described below.

Under the details section the sequence is displayed. Another option titled, blast is also there. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

2.1.6 Viewing an Activity

An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. Once you’ve successfully navigated to the activity’s home page, other than the parameters described in the general section, you’ll be able to view a few other parameters, which are described below.

Under the details section you can view the parameter titled, time ended. Time ended, is when an activity is deemed to have been ended by an entity, known as trigger. The activity no longer exists after its end. Any usage, generation, or invalidation involving an activity precedes the activity’s end. An end may refer to a trigger entity that terminated the activity, or to an activity, known as ender that generated the trigger.

2.1.7 Viewing an Agent

An agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent’s activity. Once you’ve successfully navigated to the activity’s home page, you view the information is mentioned in the general section.

2.2 Downloading the Information

Once you would’ve navigated successfully to the records’s home page, there would be a download option on the left, in a dropdown format.

Following are the types of formats that you may be able to download a record:

Note: Not all the record types may be downloaded in all formats.

Type Description
SBOL The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology.
Combine Archive A COMBINE archive is a single file containing the various documents (and in the future, references to documents), necessary for the description of a model and all associated data and procedures. This includes for instance, but not limited to, simulation experiment descriptions, all models needed to run the simulations and associated data files. The archive is encoded using the Open Modeling EXchange format (OMEX).
GFF3 The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines.
FASTA In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a near universal standard in the field of bioinformatics.
Image Image is a capture of the Visbol display at the top of the page.

Additional download options may be available via the use of download plugins.