Skip to content

Latest commit

 

History

History
318 lines (227 loc) · 10.2 KB

olddocs.rst

File metadata and controls

318 lines (227 loc) · 10.2 KB
Raw

## 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

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 description

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

Cmd

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

GRID ID

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

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 and uses 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 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)