TRIN Wiki content is created and moderated by (research) biodiversity communities both for prepublication research and the collaborative documentation of published taxa.

It is organised around specific projects which vary in their maturity and target audience. Some contain information put together for public consumption. Others are moderated or closed spaces, in which taxonomic projects collaborate on their own business prior to formal publication.

These projects have provided templates (some pre-release) for

Full advantage is taken on the Foswiki's capabilities including
  • the ability to create fields with configurable structure to make marked up content,
  • scripts,
  • plugins
to buildweb applications/patterns.Details about how Foswiki works can be found elsewhere (e.g.System/WebHomeandhttp://fosorg/ ).

Content Structure

....is stored in discrete pages (topics)aka a Document Oriented Store --which can be presented as html as well as other forms.Each topic
  • can be composites of many other topics
  • is version controlled
  • is programmable
  • is linked to other topics
and can include
  • page elements such as fields and attributes (described below)
  • semantic references to other topics in this wiki
  • citations
  • the usual suite of images and attachments
  • linked data (from provides such as ALA/NSL/WORMS)
  • maps (from openlayers map servers (especially ALA )
  • links to (competing) phylogenetic trees (newick/nexus or nexml - eventually)
The core content store is text based with a Mongodb cache for speed.

We are developing further our capability to formally and semantically describe fields on topics and their relationships on the basis of meaning and similarity ( through Wallace Core and Taxon Profiles Project).

Fields ...

Include

i) Field name,

ii) its attributes,

iii) display title and

iv) value.

Here is an example of how they are natively stored:
 

META:FIELD{name="Sponge_Sp" attributes="H" title="Sponge_Sp" value="Sp0006"}
META:FIELD{name="Sponge_Genus" attributes="" title="Sponge_Genus" value="Cinachyrella"}
META:FIELD{name="Sponge_Species" attributes="" title="Sponge_Species" value="australiensis"}
META:FIELD{name="Sponge_Authority" attributes="" title="Sponge_Authority" value="(Carter, 1886)"}
META:FIELD{name="Sponge_FullName" attributes="H" title="Sponge_FullName" value=""}
META:FIELD{name="Sponge_GrowthForm" attributes="" title="Sponge_GrowthForm" value="more or less spherical, short basal attachment."}
META:FIELD{name="Sponge_Colour" attributes="" title="Sponge_Colour" value="yellowish-brown exterior, sometimes brighter or paler, on deck; beige to grey in ethanol."}
META:FIELD{name="Sponge_Oscules" attributes="" title="Sponge_Oscules" value="numerous, moderately small, in porocalyces, evenly distributed over surface, sometimes inconspicuous."}
META:FIELD{name="Sponge_Texture" attributes="" title="Sponge_Texture" value="firm, harsh, incompressible."}
META:FIELD{name="Sponge_SurfaceOrnamentation" attributes="" title="Sponge_SurfaceOrnamentation" value="opaque, hispid; even, prominently hispid, with scattered porocalyces, covered in fine silt layer."}
META:FIELD{name="Sponge_EctosomalSkeleton" attributes="" title="Sponge_EctosomalSkeleton" value="membranous, with distinct multispicular bundles of megascleres radially penetrating surface."}

Topics include other metadata. For instance all wiki pages contain basic page meta datasuch as
 

..... specify associations between pages in the form of a triple with the option of the inclusion of a supporting citation.The first part of the triple is taken as the subject of the pagein which the assertion is made.

For example,

Wightman(2006) reported thatAvicenna Integra is found to occur with Sonneratia alba, Acanthus ebracteatus, Acanthus ilicifolius, and Avicennia marina.

Is coded as the following 4 tripples with citations
   [ [OccursWith::Sonneratia_alba{Cite::Wightman_2006}][<em>Sonneratia alba</em>]], [[OccursWith::Acanthus_ebracteatus{Cite::Wightman_2006}][<em>Acanthus ebracteatus</em>] ]
    [ [OccursWith::Acanthus_ilicifolius{Cite::Wightman_2006}][<em>Acanthus ilicifolius</em>]], [[OccursWith::Avicennia_marina{Cite::Wightman_2006}][<em>Avicennia marina</em>] ]
   

Linked Data....

...sources are used wherever possible. LSID'sor other URN's are stored on the pages where linked data is to be included. We are in the process of implementing recipes / procedures for each webserviceor data provider.So far, only a few have been implemented. These include NSL, some WORMS, and some ALA webservices.

It is sometimes the case that some local linked data sets are partially covered by linked data services. This is the case with specimen occurrence records for some projects such as SpongeMaps? which do not fully overlap with OZCAM.

Responses are cached.This is for more than optimal performance. It is important that any annotations and writing in a given page be kept in context. We are building tools to detect when a linked datasource has changed so that content needs to be reviewed along with reports and user interfaces to make this easy to maintain.

Permanent Identifiers...

Wiki pages (Topics)have permanent identifiers.LSIDs and other URNs are used to store for pages where linked data is sourced.

Content presentation / delivery / Serialisation

Individual page elementsandentire pagescan be requested viawebservices.Theycan be presented/serialised in a variety of forms including
  • html
  • JSON -- under dev.
  • mockxml
  • etc
e.g. a JSON serialisation of http://trin.org.au/bin/query/Marine/Sponges/Taxa/OTU0006/topic.json contains....

   "FIELD": [
        {
            "value": "Sp0006",
            "name": "Sponge_Sp",
            "title": "Sponge_Sp",
            "attributes": "H"
        },
        {
            "value": "Porifera",
            "name": "Sponge_Phylum",
            "title": "Sponge_Phylum",
            "attributes": ""
        },
        {
            "value": "more or less spherical, short basal attachment.",
            "name": "Sponge_GrowthForm",
            "title": "Sponge_GrowthForm",
            "attributes": ""
        },
        {
            "value": "yellowish-brown exterior, sometimes brighter or paler, on deck; beige to grey in ethanol.",
            "name": "Sponge_Colour",
            "title": "Sponge_Colour",
            "attributes": ""
        },
        {
            "value": "numerous, moderately small, in porocalyces, evenly distributed over surface, sometimes inconspicuous.",
            "name": "Sponge_Oscules",
            "title": "Sponge_Oscules",
            "attributes": ""
        },
        {
            "value": "firm, harsh, incompressible.",
            "name": "Sponge_Texture",
            "title": "Sponge_Texture",
            "attributes": ""
        },
        {
            "value": "opaque, hispid; even, prominently hispid, with scattered porocalyces, covered in fine silt layer.",
            "name": "Sponge_SurfaceOrnamentation",
            "title": "Sponge_SurfaceOrnamentation",
            "attributes": ""
        },
        {
            "value": "membranous, with distinct multispicular bundles of megascleres radially penetrating surface.",
            "name": "Sponge_EctosomalSkeleton",
            "title": "Sponge_EctosomalSkeleton",
            "attributes": ""
        },
        {
            "value": "radially arranged bundles diverging at periphery, with moderately heavy collagen containing abundant sigmaspires (sometimes lost).",
            "name": "Sponge_ChoanosomalSkeleton",
            "title": "Sponge_ChoanosomalSkeleton",
            "attributes": ""
        },
        {
            "value": "oxeas: ~7000-9000 µm; anatriaenes: >1000 µm; protriaenes: >1000 µm.",
            "name": "Sponge_Megascleres",
            "title": "Sponge_Megascleres",
            "attributes": ""
        }.......

Content Semantics

...of page elements are described by webservices using WallaceCore which (when released) provide webservices with formal descriptions and cross linkages of fields

Notification / Change tracking

It is possible to receive notifications of changes to both individual pages and collections of pages (for a project) via
  • email
  • AtomPub

Access Control

..is determined by content providers. Each project can have several nominated wiki masters.

Access is controlled through standard Foswiki access control measures via users and groups specific to a purpose.

Contribution

...generally requires a wiki account.It is

Some projects use anonymous comments 'authenticated' via Disqus othersvia Captchausage of which has been light to date.

Terms of usage and attribution

.. is determined by each project.For the most part it is open,some projects are closed whilst others contain a mix of closed and open content.

Each projecthasa place to specify their own terms of use e.g.Mangroves/TermsOfUse

It is clear some work is required here.

e.g. a JSON serialisation of http://trin.org.au/bin/query/Marine/Sponges/Taxa/OTU0006/topic.json

contains....
"FIELD": [

{

"value": "Sp0006",

"name": "Sponge_Sp",

"title": "Sponge_Sp",

"attributes": "H"

},

{

"value": "Porifera",

"name": "Sponge_Phylum",

"title": "Sponge_Phylum",

"attributes": ""

},

{

"value": "more or less spherical, short basal attachment.",

"name": "Sponge_GrowthForm",

"title": "Sponge_GrowthForm",

"attributes": ""

},

{

"value": "yellowish-brown exterior, sometimes brighter or paler, on deck; beige to grey in ethanol.",

"name": "Sponge_Colour",

"title": "Sponge_Colour",

"attributes": ""

},

{

"value": "numerous, moderately small, in porocalyces, evenly distributed over surface, sometimes inconspicuous.",

"name": "Sponge_Oscules",

"title": "Sponge_Oscules",

"attributes": ""

},

{

"value": "firm, harsh, incompressible.",

"name": "Sponge_Texture",

"title": "Sponge_Texture",

"attributes": ""

},

{

"value": "opaque, hispid; even, prominently hispid, with scattered porocalyces, covered in fine silt layer.",

"name": "Sponge_SurfaceOrnamentation",

"title": "Sponge_SurfaceOrnamentation",

"attributes": ""

},

{

"value": "membranous, with distinct multispicular bundles of megascleres radially penetrating surface.",

"name": "Sponge_EctosomalSkeleton",

"title": "Sponge_EctosomalSkeleton",

"attributes": ""

},

{

"value": "radially arranged bundles diverging at periphery, with moderately heavy collagen containing abundant sigmaspires (sometimes lost).",

"name": "Sponge_ChoanosomalSkeleton",

"title": "Sponge_ChoanosomalSkeleton",

"attributes": ""

},

{

"value": "oxeas: ~7000-9000 µm; anatriaenes: &gt;1000 µm; protriaenes: &gt;1000 µm.",

"name": "Sponge_Megascleres",

"title": "Sponge_Megascleres",

"attributes": ""

},