Re: [Tdwg-obs] Antw: Re: On observation definition / moving forward
Hi Sabine,
What you describe for plants is very much like what we often find in vertebrates.
At any given sampling event, you may want to characterise differently units that belong to the same taxon. In birds, if you are talking about banding (ringing) data, you typically want to record the characteristics of each individual (mass, body measurements, sex, band number, etc.). For that reason, a schema needs to allow repeating the same taxonomic unit multiple times in the same sampling event, each record with its own characteristics. On the other hand, if you have a group of organisms that all share exactly the same characteristics, it makes a lot more sense to have a field that tell you how many times this unit was repeated, rather than have separate records for each.
For all biodiversity monitoring, there are common fields that will allow you to describe what your unit is (taxonomic fields), in addition to other fields such date, time, location, etc. But each discipline will also have its own requirements. Bird banders typically do not care about soil or water pH, and you surely do not need to describe whether your units had a brood patch.
In a schema, the way to handle this is to put everything that is common to all disciplines in the core list of fields. DarwinCore already gives a number of those fields, but there are more common fields that can be added (DarwinCore was initially designed for museum specimens). Everything that is specific to a limited number of disciplines then need to be part of a schema extension. In birds monitoring, we think so far that this will represent about 4 or 5 different extensions (one for surveys, one for bird banding, one for nest records, etc.). The agrobiodiversity community will have to work on it's own extensions, as will other communities (which don't necessarily have to be taxon-based).
Cheers Denis
Denis Lepage, Senior Scientist/Chercheur sénior National Data Center/Centre national des données Bird Studies Canada/Études d'Oiseaux Canada PO Box/B.P. 160, Port Rowan, ON N0E 1M0 519-586-3531 ext. 225, fax/téléc. 519-586-3532
-----Original Message----- From: Tdwg-obs-bounces@lists.tdwg.org [mailto:Tdwg-obs-bounces@lists.tdwg.org]On Behalf Of SABINE ROSCHER Sent: 10 February 2006 9:11 AM To: Tdwg-obs@lists.tdwg.org Subject: [Tdwg-obs] Antw: Re: On observation definition / moving forward
Hello,
We work in the field of agrobiodiversity, e.g. crop wild relatives. For us the combination of oberservation data and samples is very important.
We consider the unit as central element, which can be a part of an organism, an ogranism, or a group of organisms. The reason for going under the level of organism is that sometimes the plant with all roots etc. can be quite larger than the part that is observed and recorded for a certain location.
This describes the line we think along : "A unit in our context is uniquely identified by time, place(site) and taxonomy. In addition a particular unit could be sampled to further assist in characterising it. Such samples could be (1) seed samples/planting material (classical ex situ accessions), (2) photos or (3) herbarium vouchers."
UNIT {time, site, taxonomy} (+ sample)
(With regard to the prior discussion I agree that we also have to handle legacy data with missing entries for time and place.)
Sabine
Sabine Roscher 513 - Informations- und Koordinationszentrum für Biologische Vielfalt (IBV) Bundesanstalt für Landwirtschaft und Ernährung Deichmanns Aue 29, 53179 Bonn Tel.: +49 (0)228 6845-3235 (oder -3237) Fax: +49 (0)228 6845-3787 E-Mail: sabine.roscher@ble.de Internet: www.ble.de weiterführende Information: www.genres.de
Steve Kelling stk2@cornell.edu 09.02.2006 18:55 >>>
Hello, I really like the improvements made on the definition, and I might suggest that I put it up on the TDWG-obs website http://www.avianknowledge.net/tdwg. I think we still need to define occurrence, and I think that Arthur Chapman's "species occurrence data" gets us most of the way there. My sense is that the elaborations need to be expanded a bit more. For example, data collection event. I suggest that we include in the definition some information about time, minimum required data, and so forth. These definitions can be longer and more detailed than the observation definition. So taking data collection event: An event, during or after which at least the minimum required data were recorded.
Can we identify the minimum required data? For us it is: who the collector is where the information was collected (and should refer to occurrence information and all of the discussion with it) when the data and time what was observed (and how many) effort distance covered, time spent etc. I'm sure there are other data for the minimum required data and this is worth discussion.
We should also discuss the event. For example, one of ours and Bird Studies Canada projects (Project FeederWatch) the event can last 2 days.
We also need to think about whether we want to include protocol. In our definitions no protocol (incidental observation) is also a protocol.
Anyway, thanks for the improvements on the definition of observation. I (like Lynn) look forward to discussing some of these other issues.
Steve
At 05:03 PM 2/8/2006 -0500, you wrote:
With only comments from Bob & Arthur (thanks!), the latest version of observation definitions is as follows:
"An observation characterizes the evidence for the presence
or absence
of an organism or set of organisms through a data collection
event at a
location. Observations are not necessarily independent and could be linked via characteristics such as time, place, protocol, and co-occurring organisms."
With the following draft elaborations for various terms
(many thanks to
Bob Peet for providing most of these draft definitions):
- occurrence
"Occurrence" has been changed to "evidence for the presence
or absence".
The key idea is that the organism or set of organisms was either detected or not. We also need to provide an opportunity for the recorder to note the certainty.
As an aside, recall we need to support minimalist protocols (e.g. "organism/community (not)seen in field", "organism heard in field", "scat seen in field", "tracks seen in field", "museum collection".)
- data collection event
An event, during or after which at least the minimum
required data were
recorded.
- location
Ideally, at least geocoordinates plus an accuracy term.
Since there is a
considerable amount of historical / legacy data that does
not presently
have a georeference yet has valuable information that should
be included
in observation databases and shared, we cannot at this time
require data
to be in a GIS format.
I (Lynn) suggest: (a) Location information be required, preferably geocoordinates and mapping precision, but if not available then a text
description and the
finest level of geolocation using the Darwin Core attributes.
(b) Location data include the representation of observations
as point,
line, or polygon data (with the necessary spatial metadata).
- entity
Dropped from the definition of observation.
- could be linked
Can have a pointer or pointers to other observations,
thereby creating
aggregate observations. Note that commonality of date, time, place, etc. is not sufficient in that the none of the observation authors explicitly made the connection
Please share your comments / thoughts on all of the above definitions with this email list.
If people are generally comfortable with the above as working defintions, then I'd like to propose that we move into the
fun part of
identifying attributes to be developed into a schema.
Thank you - Lynn
Lynn Kutner Data Management Coordinator NatureServe phone: (303) 541-0360 email: lynn_kutner@natureserve.org http://www.natureserve.org/
Tdwg-obs mailing list Tdwg-obs@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-obs_lists.tdwg.org
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Denis, I agree with your sentiments here, and it is the only way we can handle the vast amount of differences. More than people expect, however, can be generalised for different groups. Allan Allison and myself had an intereting example of this in Indonesia many years ago where we were working with foresters, fisherman, insect people and botanists, and trying to look at the common denominator in as many fields as possible. One that came up was collecting method where virtually every group saw their group as so specialised and wanted fields that would only apply to them (fishermen for example for net type, size etc.) We eventually got them all to see that we could use just "collecting method" with a different set of terms for each group.
But I think Sabine has an additional point that needs to be covered.
If I read Sabine rightly, she is talking about what the observation may be and not necessarily the aspects of that observation (measurements etc.). I think there are perhaps two aspects to what she is saying.
I can see the need for observation of "scat" or "hair" for mammals, "pupa" "lavae" for insects, "fruit" for plants, "nest" for a bird, etc. where these may have been observed separately from the main animal/plant etc. It is an observation, but not an obseration of the whole animal/plant, etc.
I am not sure that 'Unit' is the best term, though - worth discussing.
Cheers
Arthur D. Chapman Toowoomba, Australia
From Denis Lepage dlepage@bsc-eoc.org on 10 Feb 2006:
Hi Sabine,
What you describe for plants is very much like what we often find in ver> tebrates.
At any given sampling event, you may want to characterise differently un> its that belong to the same taxon. In birds, if you are talking about ba> nding (ringing) data, you typically want to record the characteristics o> f each individual (mass, body measurements, sex, band number, etc.). For> that reason, a schema needs to allow repeating the same taxonomic unit
multiple times in the same sampling event, each record with its own
char> acteristics. On the other hand, if you have a group of organisms that al> l share exactly the same characteristics, it makes a lot more sense to h> ave a field that tell you how many times this unit was repeated, rather
than have separate records for each.
For all biodiversity monitoring, there are common fields that will allow> you to describe what your unit is (taxonomic fields), in addition to ot> her fields such date, time, location, etc. But each discipline will also> have its own requirements. Bird banders typically do not care about soi> l or water pH, and you surely do not need to describe whether your units> had a brood patch.
In a schema, the way to handle this is to put everything that is common
to all disciplines in the core list of fields. DarwinCore already gives a number of those fields, but there are more common fields that can be
a> dded (DarwinCore was initially designed for museum specimens). Everythin> g that is specific to a limited number of disciplines then need to be pa> rt of a schema extension. In birds monitoring, we think so far that this> will represent about 4 or 5 different extensions (one for surveys, one
for bird banding, one for nest records, etc.). The agrobiodiversity
comm> unity will have to work on it's own extensions, as will other communitie> s (which don't necessarily have to be taxon-based).
Cheers Denis
Denis Lepage, Senior Scientist/Chercheur sénior National Data Center/Centre national des données Bird Studies Canada/Études d'Oiseaux Canada PO Box/B.P. 160, Port Rowan, ON N0E 1M0 519-586-3531 ext. 225, fax/téléc. 519-586-3532
-----Original Message----- From: Tdwg-obs-bounces@lists.tdwg.org [mailto:Tdwg-obs-bounces@lists.tdwg.org]On Behalf Of SABINE ROSCHER Sent: 10 February 2006 9:11 AM To: Tdwg-obs@lists.tdwg.org Subject: [Tdwg-obs] Antw: Re: On observation definition / moving forward
Hello,
We work in the field of agrobiodiversity, e.g. crop wild relatives. For us the combination of oberservation data and samples is very important.
We consider the unit as central element, which can be a part of an organism, an ogranism, or a group of organisms. The reason for going under the level of organism is that sometimes the plant with all roots etc. can be quite larger than the part that is observed and recorded for a certain location.
This describes the line we think along : "A unit in our context is uniquely identified by time, place(site) and taxonomy. In addition a particular unit could be sampled to further assist in characterising it. Such samples could be (1) seed samples/planting material (classical ex situ accessions), (2) photos or (3) herbarium vouchers."
UNIT {time, site, taxonomy} (+ sample)
(With regard to the prior discussion I agree that we also have to handle legacy data with missing entries for time and place.)
Sabine
Sabine Roscher 513 - Informations- und Koordinationszentrum für Biologische Vielfalt (IBV) Bundesanstalt für Landwirtschaft und Ernährung Deichmanns Aue 29, 53179 Bonn Tel.: +49 (0)228 6845-3235 (oder -3237) Fax: +49 (0)228 6845-3787 E-Mail: sabine.roscher@ble.de Internet: www.ble.de weiterführende Information: www.genres.de
Steve Kelling stk2@cornell.edu 09.02.2006 18:55 >>>
Hello, I really like the improvements made on the definition, and I might suggest that I put it up on the TDWG-obs website http://www.avianknowledge.net/tdwg. I think we still need to define occurrence, and I think that Arthur Chapman's "species occurrence data" gets us most of the way
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participants (2)
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Denis Lepage -
tdwg＠achapman.org