Biodata Management Guide

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Kete

Kete is an open source online community platform that is used as a biodiversity object repository for  T.E.R:R.A.I.N (Taranaki Educational Resource: Research, Analysis and Information Network). Kete supports upload/download of standard metadata files conforming to Dublin Core/ANZLIC/ISO19115.

Kete's benefits include:

  • a built-in Open Archive Initiative Protocol for Metadata Harvesting (OAI-PMH) Repository of metadata for all public items in the system. Excellent for sharing metadata with services such as Digital New Zealand.

  • an customizable system for describing the site's items

    • add new topic types to describe what the data is about, e.g. one could add a topic type for a "sighting"

    • site administrator's may add new "extended fields" to be associated with topic types or content types (images, audio recordings, videos, documents, web links, or discussion posts), e.g. an administrator could add a "species" field to the  "sightings" topic type

    • extended fields have a number of rich field type options, e.g. an administrator could add a "location" field that records latitude and longitude coordinates for the sighting via a Google map

  • embedded metadata harvesting from uploaded files, e.g. grab geographic coordinates embedded in images recorded with a GPS equipped digital camera

  • multiple systems for grouping related materials either informally, such as tagging, or through directly mapping relationships between items via their fields

  • plays well with others. Each Kete site is able to share its material via search services available to other software (via the OpenSearch pattern). Kete 1.3 and above has the ability to pull in material from external search sources, such as other Kete sites or Digital New Zealand

Discuss Kete in the Dataversity Public Discussion Group

Further comments about Kete's features can be found in this post in Data.govt.nz.

Case Study: How Kete is used with T.E.R:R.A.I.N

The T.E.R:R.A.I.N Project

Each of the community groups has specific requirements for collecting and displaying biodata. All groups collect information about species, locations and numbers, historic and current. All require a mapping service, and would like their information to be available in an approved standardised format not just for their own use, but to the planners, policy analysts and the resource consent process. Groups wish to see information they collect being used for biodiversity management. T.E.R:R.A.I.N seeks to make data available.

All the groups have highly knowledgeable staff and volunteers (many retired) who can contribute to local and national datasets and help avoid the phenomenon of “generational amnesia” which besets government departments with the rapid staff changeover seen in recent decades. The concept of ‘citizen scientist’ contributing to national datasets is important. In many cases the ‘citizen’ experts have knowledge which we cannot afford to loose. Cooperation with authorities to make use of the citizen information is vital. A metadata entry to flag the qualifications/expertise of the observer allows the value of contributions to be assessed – indicative >>> expert.

The design of the databases and ketes are specific to the aims and function of each group,

  • Public or private maps may be served depending with whom they wish to share data
  • Some species do not need to be publicly advertised to collectors/smugglers, but the information is useful for reserve selection (Marxan / Marzone / Zonation) on land or sea, biodiversity management, or the consent process.
  • The concept of focus-groups or stakeholder workshops where data is entered to specific areas of the map. The consultative process can achieve not only data-gathering but scenario testing.
  • GIS layers may hold not only species data but information about community values – historical values and aesthetics which provide information for decision support tools such as NatureServe Vista and Community Viz.

An example - the plant database for Pukekura Park: This contains many fields and links to other tables of information which are not needed for public viewing (Genus /species / variety /Cultivar /date planted / commemorative planting / historic links / Burstall notable tree mensuration records/  Medbury tree list / Cory Smith mensuration records / arboricultural records / bird food phenology / ethnobotany / related epiphytes / related fungi /  related insects).

The community group supplies the plant identification, parses scanned items such as mensuration reports, and research historical documents. The NPDC staff can keep the arboriculture tables in-house. These together with sequential mensuration reports and images of the Park will allow staff and landscape architects to plan the successional plantings in the Park. Together, the factors in the database may be used to evaluate not just the asset value but the cultural value in management and planning.

Several T.E.R:R.A.I.N groups encourage visitors with information not specific to current projects to contribute to NZBRN or ARDS (amphibians and reptiles) databases.

Kete as a data catalogue, as used with T.E.R:R.A.I.N.

Kete is used in the T.E.R:R.A.I.N (Taranaki Educational Resource: Research, Analysis and Information Network) project http://www.terrain.net.nz .

Three of the community groups have their own kete. The ‘Friends of Pukekura Park’ use the most recent software development features whilst others run on the version used by the National Libraries (APN) system.

Kete provides T.E.R:R.A.I.N. with the following.

  • Repository for all file types we have tried – images, sound, movies, documents
  • Bulk file uploads
  • Options to add descriptions/metadata fit-to-purpose – in addition to standard Dublin Core etc.
  • The metadata of the files is maintained when they are downloaded from kete to a p.c.
  • Kete provides the opportunity to design the repository to suit the purpose. You may choose to create sub-directories (baskets) pertaining to specialised topics, case histories, an author, or specific copyright… Pukekura Park is organised around the main contributors and their copyright preferences. The kete Nga Motu is organised according to marine subjects.
  • Within each basket you may set up topics, and provide specific ‘extended fields’, and allow choices. For example, http://kete.pukekura.org.nz designed different extended fields to be available for topics on historical events and plant life. If you are adding a topic about a person you will need ‘event’ rather than ‘plant species’.
  • Searches may be conducted within the kete as a whole, or within a basket;
  • You may subscribe to RSS feeds containing key terms that you want information on.
  • The kete can display any RSS feeds you wish to set up – e.g. Pukekura Park extends the available resources search generally to the Alexander Turnbull Library,
  • And specific searches e.g “kauri disease” can be supplemented by requested searches to display more resources from other sources e.g. ‘Digital New Zealand’ alongside the results from the kete.
  • Sorting and searches may be done by topic, resource type, tag, keywords, author etc.
  • The feature of adding links between repository items means that a document in the “Site” basket can be identified as of high relevance to other topics in other baskets. See the Topic ‘Plants and Trees of Pukekura Park’ http://kete.pukekura.org.nz/site/topics/show/50-plants-and-trees-of-pukekura-park – where items from many baskets are related - mensuration reports, magazine articles, comments on Park development plans, and images taken for a variety of purposes.
  • Kete images or documents may be opened in other applications – such as the image seen on the front page image of www.pukekura.org.nz – this is a link to file http://kete.pukekura.org.nz/image_files/0000/0000/2537/DSCN0784.JPG  . This means that a file is loaded once to kete, and used in multiple applications.
  • Geographic coordinates from cameras with GPS data – we aim to set up this metadata harvest for the ‘Friends of Te Henui’ who take a lot of pictures of plants and wildlife which we need to locate on maps.
  • Embedded forms: An excellent tool for running on-line SurveyMonkey questionnaires, or Google Apps (for registered users).

How T.E.R:R.A.I.N. provides two-way access between the GIS and Kete.

See a short demo on http://www.taranakiwiki.com/moodle/file.php/10/Kete_Pukekura/Pukekura_Park_plants_demo.mp4 (explanatory notes below movie)

2.1. Linking records to specific locations, and visa versa, is possible through the on-line maps. T.E.R:R.A.I.N. operates using a variety of methods.

2.1.1. The Pukekura Park maps are hosted by NPDC GISBoost http://gis.npdc.govt.nz/fopp/WebPages/Map/MapViewer.aspx . You can search for plants in the Park using specific or common names. The results are mapped and attributes provide a link back to the kete information.

In kete, if the plant described in the document has been mapped in the Park, then a link to the map is offered through the extended field “Search Plant Species GIS”. The GISBoost then displays the location of all mapped plants of that species, e.g Search for Vitex lucens = 14 trees are mapped, there are 15 images, 1 web link and 11 documents.

2.1.2 All other T.E.R:R.A.I.N. maps use open source software Geoserver and OpenLayers to provide maps using a variety of imagery sources. The group which has most information on kete is ‘Friends of Te Henui’, and is poised to publish live maps with links directly between the GIS maps to kete (as hyperlinked files) and from the kete to the GIS map using an action for an automated search of kete.

The Nga Motu Marine Reserve Society has images stored in kete which are directly opened by clicking the flagged point on the map. Eg the image of a penguin roost site is http://ketenewplymouth.peoplesnetworknz.info/image_files/0000/0000/1163/Tapuae_Marine_Reserve_41208_penguins_historic_climbing_13_1.JPG is displayed directly from the kete. The map of Bell Block penguin boxes and pest traps http://125.236.243.110:8080/geoserver/openlayers/examples/bellblkpenguinbox.html  links directly to the images held in kete http://ketenewplymouth.peoplesnetworknz.info/site/topics/show/186-penguin-nesting-boxes .

2.2 Creating records in an on-line database for display on a web-map:

‘Point and click’on-line data entry to GIS database uses a map associated with a data-entry form: The Nga Motu Marine Reserve Society in conjunction with Forest & Bird request that the public enter sightings and historic records of Little Blue Penguins in Taranaki. http://www.terrain.net.nz/nga-motu-marine-reserve-society-group/research-projects-along-the-coast.html The method is available for the coastline between Motunui and Oakura for which we have suitable aerial imagery. With assistance from TRC the imagery will soon be available for all of Taranaki but in the meantime we are using an on-line form in kete (login secured) which feeds Google Apps, thence update to GIS database .

A Google Apps data-entry form is also used in the kete Pukekura Park for wildlife records e.g. http://kete.pukekura.org.nz/60_springs/topics/show/60-amphibians