Open peterdesmet opened 2 years ago
Note that the start eventRemarks are currently based on a number of fields:
Resulting in e.g.:
UvA-BiTS tag attached by harness to free-ranging animal | Found dead in Sint-Maartensdijk (NL) on 2018-08-24, last active day is 2018-08-23.
This will likely be empty if any of the fields are empty.
I can look at this next week, but one thing to think about: The deploy start/end times are sometimes based on something other than a human observation. For the deploy-on time, we can assume with current methods that the tag had to be attached by a person, and therefore assume it at least approximates the time of a human observation. For the deploy-off-time, this is regularly used to define the end of the reliable tracking data, e.g., to exclude locations from the track determined to have been recorded after the tag stopped moving or sending reliable data. Even when tags are physically retrieved, this often happens after an animal has died, or after it has been automatically released from the animal, so doesn't necessarily represent an observation of the live animal.
Hmm, interesting point. I'll reference your comment in #10.
Addressed. @sarahcd can you go over the list and check off the ones that you think make sense to exclude from DwC (I indicated them crossed out). We should then go over the remaining ones to see what to do with those.
Sorry for the delay. I am breaking these down based on the entity they describe in Movebank, since this could impact how to code transformation to DwC.
Possible mappings added from above have notes in italics. We can discuss whether to implement any additions to the current version, and I could propose specifics in the sql.
Terms describing the animal
animal-comments
: start occurrenceRemarks? SD: or add start organismRemarksanimal-death-comments
: SD: could include in start organismRemarks?animal-earliest-date-born
: SD: could include in start organismRemarks animal-exact-date-of-birth
: SD: could include in start organismRemarksanimal-id
: organismID, part of eventIDanimal-latest-date-born
: SD: could include in start organismRemarksanimal-nickname
: organismNameanimal-ring-id
: include, where? could include in start organismRemarks
@tucotuco: For a more specific mapping (not necessarily to use here): Could a bird band/ring number be stored using previousIdentifications? These IDs are used by ringing programs and are sometimes stored there with other information, could be associated with related samples, etc. The band is often but not always attached at the same time as the tracking tag, so 'previous' isn't necessarily accurate, but it's close.animal-sex
: sexanimal-taxon
: scientificNameanimal-taxon-detail
SD: could include in start organismRemarksTerms describing the tag
tag-beacon-frequency
~tag-comments
~tag-failure-comments
~ endtag-id
: part of eventIDtag-manufacturer-name
: included in start eventRemarkstag-mass
: SD: could be included in start eventRemarkstag-model
: included in start eventRemarkstag-processing-type
~Terms describing the deployment, including tags and animals at the time of the deployment
alt-project-id
: SD: maybe something from ResourceRelationship could work here?animal-life-stage
: lifeStageanimal-mass
: SD: could be included in start eventRemarks animal-reproductive-condition
: reproductiveConditionattachment-type
: included in start eventRemarksbehavior-according-to
~data-processing-software
~deploy-off-date
~: enddeploy-off-latitude
~: enddeploy-off-longitude
~: enddeploy-off-person
~: enddeploy-on-date
: start eventDatedeploy-on-latitude
: start decimalLatitudedeploy-on-longitude
: start decimalLongitudedeploy-on-person
: start recordedBy? SD: agreedeployment-comments
: included in start eventRemarksdeployment-end-comments
~: enddeployment-end-type
~: enddeployment-id
~duty-cycle
~geolocator-calibration
~geolocator-light-threshold
~geolocator-sensor-comments
~geolocator-sun-elevation-angle
~habitat-according-to
~location-accuracy-comments
~manipulation-comments
~manipulation-type
: included in start eventRemarksstudy-site
: SD: could be included in start event as locationRemarks or localitytag-readout-method
SD: could be included in start eventRemarkstag-production-date
~tag-serial-no
~@sarahcd do you think including study-site
for human observations makes more sense as:
Note that for GPS observations, the locationRemarks
currently state "elevations are altitude above mean sea level"
Overview of things to tackle:
animal-comments
: Additional information about the animal that is not described by other reference data terms.
animal-death-comments
: Comments about the death of the animal.
animal-earliest-date-born
: The earliest date an animal is thought to have been born or hatched.
animal-exact-date-of-birth
: The exact date on which animal was born or hatched.
animal-latest-date-born
: The latest date an animal is thought to have been born or hatched.
animal-ring-id
: A number or color scheme for a band or ring attached to the animal. Color bands and other markings can be stored in 'animal marker ID'.
animal-mass
: The mass of the animal
deploy-on-measurements
(new field): A list of additional measurements taken during capture of the animal at the start of the deployment. Recommended best practice is to define units and use a key:value encoding schema for a data interchange format such as JSON.
animal-taxon-detail
: A more specific name and/or reference for the taxon name provided by 'animal taxon'.
study-site
: A location such as the deployment site or colony, or a location-related group such as the herd or pack name.
alt-project-id
: A name or unique identifier for a project associated with the deployment, for example a monitoring program or another data platform.
tag-readout-method
: The way the data are received from the tag.
For the animal death- I am really really hoping that vitality will be added to Darwin Core so you should be able to use that term for this.
@sarahcd do you think including
study-site
for human observations makes more sense as:* locality: https://dwc.tdwg.org/terms/#dwc:locality * locationRemarks: https://dwc.tdwg.org/terms/#dwc:locationRemarks
Note that for GPS observations, the
locationRemarks
currently state "elevations are altitude above mean sea level"
locality
for human observations sounds good to me. Also, FYI, we are in the progress of adding locality
as an event field in Movebank (e.g., for GPS records) for cases that segments of data are assigned location names. I think those should work fine together in the translation to DwC.
@sarahcd so far I have based the mapping for the start and end HumanObservations on fields I have in my datasets. It would be good however to have a mapping based on all fields potentially available in the reference data. Can you check the field where you agree that they are not useful to map (crossed out) and comment on those you think would be useful to include?
animal-comments
: start occurrenceRemarks?animal-death-comments
~: endanimal-exact-date-of-birth
~animal-id
: organismIDanimal-latest-date-born
~animal-life-stage
: lifeStageanimal-mass
~animal-nickname
: organismNameanimal-reproductive-condition
: reproductiveConditionanimal-ring-id
: include, where?animal-sex
: sexanimal-taxon
: scientificNameanimal-taxon-detail
~attachment-type
: included in start eventRemarksbehavior-according-to
~data-processing-software
~deploy-off-date
~: enddeploy-off-latitude
~: enddeploy-off-longitude
~: enddeploy-off-person
~: enddeploy-on-date
: start eventDatedeploy-on-latitude
: start decimalLatitudedeploy-on-longitude
: start decimalLongitudedeploy-on-person
: start recordedBy?deployment-comments
: included in start eventRemarksdeployment-end-comments
~: enddeployment-end-type
~: enddeployment-id
~duty-cycle
~geolocator-calibration
~geolocator-light-threshold
~geolocator-sensor-comments
~geolocator-sun-elevation-angle
~habitat-according-to
~location-accuracy-comments
~manipulation-comments
~manipulation-type
: included in start eventRemarksstudy-site
tag-beacon-frequency
~tag-comments
~tag-failure-comments
~tag-id
: part ofeventID
tag-manufacturer-name
: included in start eventRemarkstag-mass
~tag-model
: included in start eventRemarkstag-processing-type
~tag-production-date
~tag-readout-method
~tag-serial-no
~