## From curators_guide.rst Disk image format ................. Virtual machine disk image format
- 1. MUST acurately specify the format of download of type "VM image", in terms from a controlled vocabulary (see below)
Disk format | Description |
---|---|
aki | An Amazon kernel image |
ami | An Amazon machine image |
ari | An Amazon ramdisk image |
iso | An archive format for the data contents of an optical disc, such as CD-ROM |
qcow2 | Supported by the QEMU emulator that can expand dynamically and supports Copy on Write |
raw | An unstructured disk image format; if you have a file without an extension it is possibly a raw format |
vdi | Supported by VirtualBox virtual machine monitor and the QEMU emulator |
vhd | The VHD disk format, a common disk format used by virtual machine monitors from VMware, Xen, Microsoft, VirtualBox, and others |
vmdk | Common disk format supported by many common virtual machine monitors |
Container format
- 1. MUST acurately specify the format of download of type "Container file", in terms from a controlled vocabulary (see below)
Container format | Description |
---|---|
aki | An Amazon kernel image |
ami | An Amazon machine image |
ari | An Amazon ramdisk image |
bare | The image does not have a container or metadata envelope |
docker | A docker container format |
ovf | The OVF container format |
rkt | Rocket container image |
singularity | Singularity container format |
- ## From api_attribute_model_dev.rst
"diskFormat": "raw", "diskFormat": "raw",
- diskFormat
- Required: No
- Cardinality: 1 only
- Type: ENUM
- Allowed values: (see Curators Guide)
aki
ami
ari
iso
qcow2
raw
vdi
vhd
vmdk
- containerFormat
- Required: No
- Cardinality: 1 only
- Type: ENUM
- Allowed values: (see Curators Guide)
aki
ami
ari
bare
docker
ovf
rkt
singularity
- <diskFormat>raw</diskFormat>
"diskFormat": "raw",
- "containerFormat": "docker",
- "containerFormat": "docker",
- <containerFormat>docker</containerFormat>
- "containerFormat": "docker",
## From curators_guide.rst
Short and concise textual description of the software function, e.g. "Needleman-Wunsch global alignment of two sequences."
- 1. MUST provide a terse statement of the primary purpose / function of the tool: what is done not how
- 2. MUST begin with a capital letter and end with a period ('.')
- 3. MUST NOT include tool name
- 4. MUST NOT include any of the following, unless essential to distinguish the tool from other bio.tool entries:
- general or technical terms ("software", "application", "server", "service", "SOAP", "REST", "RESTful" etc.)
- provenance information e.g. software provider, institute or person name
- 5. MUST NOT describe how good the software is (mentions of applicability are OK)
- 6. MUST NOT include URLs
- 7. SHOULD use declarative sentences (ideally a single sentence!) in the present tense
Note
- see the syntax guidelines.
A useful command pertinent to the download, e.g. for getting or installing a tool, e.g. "-s best".
- 1. MUST be a functional commmand of practical value
Unique identifier (GRID ID) of an organisation that is credited, e.g. "grid.5170.3"
- 1. MUST correctly identify a credited organisation
Note
Global Research Identifier Database (GRID) IDs provide a persistent reference to information on research organisations, see https://www.grid.ac/. If ORCID institutional identifiers become available, these will also be supported.
Telephone number of the entity that is credited, e.g. "+49-89-636-48018"
- 1. MUST specify a valid telephone number
- 2. MUST NOT specify a telephone number that is not publicly advertised as a contact point for the software, e.g. on a webpage or in a publication
- 3. MUST NOT specify a stale (obsolete) telephone number
Note
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In future, the
isPluginFor
relationship will allow specification of the tool to which the plug-in is applicable.
Note
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In future, the
isInterfaceTo
relationship will allow specification of the data resource (database portal) that a SPARQL endpoint provides an interface to.
Note
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In future, the
includes
relationship will allow specification of the tools that are included in a suite.
Note
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In future, the
isInterfaceTo
anduses
relationships will allow specification of the tools that a web application provides an interface to or uses.
Note
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In future, the
isInterfaceTo
relationship will allow specification of the tool or data resource (database portal) that the web service provides an interface to.
Note
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In future, the
isInterfaceTo
relationship will allow specification of the tool that the web service provides an interface to
Note
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In future, the
includes
relationship will allow specification of the tools that are included in a workbench.
Note
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In future, the
includes
relationship will allow specification of the tools that are included in a workflow.
Tip
- biotoolsSchema allows tool relationships to be defined, but these are not yet supported in bio.tools. In the meantime, collections may be used to group together related entries.
## From api_attribute_model_dev.rst .. _short-description:
Short and concise textual description of the software function, e.g. "Needleman-Wunsch global alignment of two sequences."
- Attribute name
- shortDescription
- Required
- No
- Type
- String
- Restrictions
Min length: 10
Max length: 100
Example
# XML
<shortDescription>Needleman-Wunsch global alignment of two sequences.</shortDescription>
# JSON
"shortDescription": "Needleman-Wunsch global alignment of two sequences."
Note
- minimum 10 and maximum 100 characters.
- line feeds, carriage returns, tabs, leading and trailing spaces, and multiple spaces are not allowed / will be removed.
- see the curation guidelines.
- cmd
- Required: No
- Type: String
- Restrictions: min length: 1, max length: 100
- <cmd>n/a</cmd>
"cmd": "n/a",
- gridId
- Required: No
- Type: String
- Restrictions: pattern: grid.[0-9]{4,}.[a-f0-9]{1,2}
- <gridId>grid.5170.3</gridId>
"gridId": "grid.5170.3",
- tel
Required: No
Type: String
Restrictions: min length: 5, max length: 50
<tel>12345678</tel>
- "tel": "12345678"
"tel": "123456798",
"gridid": "test",
Example
# XML
<link>
<isAvailable>Not available</isAvailable>
<type>Repository</type>
</download>
# JSON
"link":
[
{
"isAvailable": "Not available"
"type": "Repository"
}
]
Note
- if a link of a certain type is known to not be available, this can be specified using the
isAvailable
attribute (see Example)
Example
# XML
<download>
<isAvailable>Not available</isAvailable>
<type>Source code</type>
</download>
# JSON
"download":
[
{
"isAvailable": "Not available"
"type": "Source code"
}
]
Note
- if a download link of a certain type is known to not be available, this can be specified using the
isAvailable
attribute (see Example)
Example
# XML
<documentation>
<isAvailable>Not available</isAvailable>
<type>General</type>
</documentation>
# JSON
"documentation":
[
{
"isAvailable": "Not available"
"type": "General"
}
]
Note
- if a documentation link of a certain type is known to not be available, this can be specified using the
isAvailable
attribute (see Example)
Example
# XML
<publication>
<isAvailable>Not available</isAvailable>
</publication>
# JSON
"publication":
[
{
"isAvailable": "Not available"
}
]
Note
- if a publication is known to not be available, this can be specified using the
isAvailable
attribute (see Example)