API change proposal: supporting ranges in occurrence eventDate
Dear GBIF API users, /You might prefer to read this email on either GitHub or the community forum, as the formatting is probably better:/ // /GitHub issue discussion: https://github.com/gbif/gbif-api/issues/4#issuecomment-1385497157/ // /Community forum discussion: https://discourse.gbif.org/t/gbif-api-supporting-ranges-in-occurrence-eventd... A longstanding issue with the GBIF API is the interpretation and formatting of the Darwin Core term "eventDate". *Summary: instead of GBIF changing published |eventDate| values like |2009-03-18/2009-04-13| and |2010| to |2009-03-18| and |2010-01-01| respectively, we propose returning the values |2009-03-18/2009-04-13| and |2010| in the occurrence API and in downloads. Existing code/scripts that use the |eventDate| value may need to be updated.* The recommended best practise for the term is "use a date that conforms to ISO 8601-1:2019" (see https://dwc.tdwg.org/terms/#dwc:eventDate). ISO 8601-1:2019 supports date ranges, and some publishers provide these. Examples are |2000-05|, or |2007-11-13/2007-11-15|. GBIF's current interpretation changes date ranges like this to the first possible day in the range (|2000-05-01| and |2007-11-13|). At least 64 million occurrences are affected. <https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#change-to-date-interpretation> Change to date interpretation We propose changing the eventDate field in the GBIF API to support ISO 8601-1 date ranges. A range will be returned where one was provided by the publisher, either directly as a range in the |eventDate| field, or through a combination of the |year|, |month|, |day|, |startDayOfYear| and |endDayOfYear| fields. The data quality checks on dates will be improved to check for consistency between these fields: |eventDate|, |year|, |month|, |day|, |startDayOfYear| and |endDayOfYear|. These fields will only be populated if they are constant for the whole range of dates — a range spanning several days in January 2020 will have |year=2020|, |month=January| and |day=(Blank)|. |startDayOfYear| and |endDayOfYear| will also be present if the range is accurate to days. Examples: published event date intepreted eventDate int. year int. month int. day int. sdoy int. edoy 2023-01-13 2023-01-13 2023 1 13 13 13 2023-01 2023-01 2023 1 2023 2023 2023 2023-01-13/2023-01-14 2023-01-13/2023-01-14 2023 1 13 14 2023-01-13/14 2023-01-13/14 2023 1 13 14 2023-01/2023-02 2023-01/2023-02 2023 2023-01/02 2023-01/02 2023 2023/2024 2023/2024 2023-01-01/2023-12-31 2023-01-01/2023-12-31 2023 1 365 Other cases where we can unambiguously determine a date or date range will also be handled, for example a record with a |year| and |month| but no |eventDate|, or non-ISO dates like |January 2023|. <https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#api-example> API example: This record <https://api.gbif.org/v1/occurrence/1234530937> (portal link <https://www.gbif.org/occurrence/1234530937>) is published with |eventDate=2009-03-18/2009-04-13|, |year=2009|, |month=3|, |day=18|. We currently change the |eventDate|: "year":2009, "month":3, "day":18, "eventDate":"2009-03-18T00:00:00", With this proposal, we would preserve the |eventDate| but remove |day|, as it the event crosses several days: "year":2009, "month":3, "eventDate":"2009-03-18/2009-04-13", This record <https://api.gbif.org/v1/occurrence/2382954724> (portal link <https://www.gbif.org/occurrence/2382954724>) is published with |eventDate=2019-04-06T20:00:00/2019-04-10T05:00:00| and no separate |day|, |month| or |year| values. Currently, we process it to this: "year":2019, "month":4, "day":6, "eventDate":"2019-04-06T20:00:00", Instead, we propose returning this: "year":2019, "month":4, "eventDate":"2019-04-06T20:00:00/2019-04-10T05:00:00", "startDayOfYear":96, "endDayOfYear":100, <https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#searching> Searching The search and download APIs will be affected by this change. Occurrences will be returned if the occurrence date/date range is *completely within* the query date or date range. |Search: eventDate=2023-01-11 Record: eventDate=2023-01-11 -- included Record: eventDate=2023-01 -- EXCLUDED Record: eventDate=2023-01-11/12 -- EXCLUDED Search: eventDate=2023-01-11,2023-01-12 Record: eventDate=2023-01-11 -- included Record: eventDate=2023-01 -- EXCLUDED Record: eventDate=2023-01-11/12 -- included Search: eventDate=*,2023-01 (meaning "Before end of January 2023") Record: eventDate=2023-01-11 -- included Record: eventDate=2023-01 -- included Record: eventDate=2023-01-11/12 -- included Search: eventDate=2023-01,2023-01 (meaning "After start of January 2023 AND before end of January 2023") Search: eventDate=2023-01 (same meaning) Record: eventDate=2023-01-11 -- included Record: eventDate=2023-01 -- included Record: eventDate=2023-01-11/12 -- included | This implementation will avoid returning occurrences with eventDates like "2010/2021" in many queries. (There are millions of occurrences with large ranges like this.) <https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#density-maps> Density maps There is a year filter for the density/pixel maps. An occurrence from 2023-01 will be included, but an occurrence with an eventDate spanning more than a single year (like 2022-13-31/2023-01-01) will no longer be included. <https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#quarterly-analytics-globalregional-trends> Quarterly analytics, global/regional trends The quarterly analytics include calculations based on the individual dwc:year, dwc:month and dwc:day fields. The statistics will be affected where these values change or become blank. <https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#rgbif-pygbif> rGBIF, PyGBIF Both libraries will be updated as necessary to support eventDate values containing a date range. <https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#feedback> Feedback We have delayed addressing this issue for a long time, primarily due to concerns about changing the existing behaviour of the API. However, it's also one of the most frequently requested improvements to GBIF's interpretation. If you are aware of software or systems which would have problems adapting to the proposed change, please let us know, either on this mailing list, the GitHub issue, the community forum or by email to me. We will alert users in the same places when the change is ready to be tested on the test system at api.gbif-uat.org, and when the change is to be made live on api.gbif.org. Thank you, Matt GitHub issue discussion: https://github.com/gbif/gbif-api/issues/4#issuecomment-1385497157 Community forum discussion: https://discourse.gbif.org/t/gbif-api-supporting-ranges-in-occurrence-eventd...
Matthew Blissett via API-users wrote:
We propose changing the eventDate field in the GBIF API to support ISO 8601-1 date ranges. A range will be returned where one was provided by the publisher, either directly as a range in the |eventDate| field, or through a combination of the |year|, |month|, |day|, |startDayOfYear| and |endDayOfYear| fields.
I welcome the change. I recall the discussion "Occurrence Inventories" of April 29-30, 2019, reproduced below. What will happen to existing data sets, where January 01 at 00:00 is listed for unknown dates or date ranges ? Regards, Adriaan van Os ------ On 26/01/2019 12:19, Adriaan van Os wrote:
Matthew Blissett wrote:
The documentation isn't particularly clear, but you can create the month chart using the search + facet API:
https://api.gbif.org/v1/occurrence/search?facet=month&facetLimit=12&limit=0
As an example, I looked at the flight time of Nymphalis antiopa, which is known to be around April-May and August-September. The GBIF Occurrences per Month chart
shows a lot of occurrences in January. I tracked these down to Finish datasets with eventDate January 01 at 00:00 but for a valid year.
This is an unfortunate limitation of our current system. We're working on an improvement as part of a larger effort to update our occurrence indexing, but for the moment month-only or year-only dates are indexed as the first of the month/year. We don't add an issue flag to these dates, but even if we did, another limitation of the API is it's not possible to exclude issues in the fast searches or charts. We can't set an event date of e.g. 2016-00-00, as that's not a valid ISO format date, but we can look at leaving the "month" and "day" fields empty. Regards, Matt _______________________________________________ API-users mailing list API-users@lists.gbif.org https://lists.gbif.org/mailman/listinfo/api-users
Dear GBIF API users, /You might prefer to read this email on either GitHub or the community forum, as the formatting is probably better:/ // /GitHub issue discussion: https://github.com/gbif/gbif-api/issues/4#issuecomment-1735378954/ // /Community forum discussion: https://discourse.gbif.org/t/gbif-api-supporting-ranges-in-occurrence-eventd... *Event dates — upcoming API change* Early this year we announced a plan to change the way we handle the "eventDate" Darwin Core term. Date ranges formatted using the ISO 8601 standard, recommended by Darwin Core, will retain their meaning, and the API will return values like "2000-05" or "2007-11-13/2007-11-15", rather than the current behaviour of changing these values to "2000-05-01" and "2007-11-13". These changes are now visible on GBIF's test system, GBIF-UAT.org. To allow time for you to test this change against any existing software and scripts you have, we will not implement these changes on GBIF.org before early November. *API users* Users of the occurrence API will need to decide how to handle an eventDate like "1880/1889", "1910", "2000-05", "1999-11/2000-03", "2007-11-13/2007-11-15" or "2023-09-22T05:17:10/2023-09-22T12:17:10" — taking the earliest, latest or middle value, randomizing within the range, excluding them etc. To make parsing easier ranges will always be formatted using the full form and never abbreviated — always "2007-11-13/2007-11-15" and never "2007-11-13/15". It may be easier to use the individual "year", "month" and "day" fields, which will be present if the year/month/day is constant for the whole range of the eventDate — eventDate=2010-11-25/2010-12-03 will have year=2010, month=NULL, day=NULL as only the year is constant. (However, note a date like 2022-12-31/2023-01-01 covers just 2 days, but as is spans two different years the "year" field will be blank.) When searching using a range (e.g. eventDate=2005-01,2005-03) only occurrences with eventDates *entirely within* the range will be returned. *Download users* The "eventDate" column in CSV, Darwin Core and Parquet (cloud snapshot) downloads will contain the same value as in the API, for example "2023-09-22T12:17:10", "2023-09-22", "1880/1889", "1910", "2000-05", "1999-11/2000-03", "2007-11-13/2007-11-15" or "2023-09-22T05:17:10/2023-09-22T12:17:10". As with the search API, when filtering using a range (e.g. eventDate=2005-01,2005-03) only occurrences with eventDates *entirely within* the range will be returned *Data interpretation (for data publishers)* Eight Darwin Core terms record information on when an occurrence was collected or observed: - year - month - day - eventDate - eventTime - startDayOfYear - endDayOfYear - verbatimEventDate Some records will have conflicting information in these fields. Detailed documentation on how we handle the various cases is being prepared, but the general approach is to remove parts of the date that conflict, adding a RECORDED_DATE_MISMATCH issue in this case. For example, "eventDate=2005-06-01", "year=2005", "month=6" and "day=NULL" would have eventDate changed to "2005-06" and the issue added. Occurrences published with only one/some fields will have the other fields filled in automatically, where possible. We will not add an issue flag for this. All existing datasets will be reprocessed with the new algorithms as the change to the API is made for GBIF.org. *Example dataset* A dataset of test occurrences is here: https://www.gbif-uat.org/occurrence/search?dataset_key=d6167827-973d-429a-a0... providing many examples of consistent and conflicting event date fields. The scientificName is set to a summary of what the eventDate is, and the eventRemarks field has more explanation. *Feedback* Feedback is welcome on the GitHub issue, here on the mailing list, or on the Discourse forum Thanks, Matt GitHub issue discussion: https://github.com/gbif/gbif-api/issues/4#issuecomment-1735378954 Community forum discussion: https://discourse.gbif.org/t/gbif-api-supporting-ranges-in-occurrence-eventd... On 17/01/2023 15:28, Matthew Blissett via API-users wrote:
Dear GBIF API users,
/You might prefer to read this email on either GitHub or the community forum, as the formatting is probably better:/
//
/GitHub issue discussion: https://github.com/gbif/gbif-api/issues/4#issuecomment-1385497157/
//
/Community forum discussion: https://discourse.gbif.org/t/gbif-api-supporting-ranges-in-occurrence-eventd...
A longstanding issue with the GBIF API is the interpretation and formatting of the Darwin Core term "eventDate".
*Summary: instead of GBIF changing published |eventDate| values like |2009-03-18/2009-04-13| and |2010| to |2009-03-18| and |2010-01-01| respectively, we propose returning the values |2009-03-18/2009-04-13| and |2010| in the occurrence API and in downloads. Existing code/scripts that use the |eventDate| value may need to be updated.*
The recommended best practise for the term is "use a date that conforms to ISO 8601-1:2019" (see https://dwc.tdwg.org/terms/#dwc:eventDate).
ISO 8601-1:2019 supports date ranges, and some publishers provide these. Examples are |2000-05|, or |2007-11-13/2007-11-15|. GBIF's current interpretation changes date ranges like this to the first possible day in the range (|2000-05-01| and |2007-11-13|).
At least 64 million occurrences are affected.
<https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#change-to-date-interpretation>
Change to date interpretation
We propose changing the eventDate field in the GBIF API to support ISO 8601-1 date ranges. A range will be returned where one was provided by the publisher, either directly as a range in the |eventDate| field, or through a combination of the |year|, |month|, |day|, |startDayOfYear| and |endDayOfYear| fields.
The data quality checks on dates will be improved to check for consistency between these fields: |eventDate|, |year|, |month|, |day|, |startDayOfYear| and |endDayOfYear|. These fields will only be populated if they are constant for the whole range of dates — a range spanning several days in January 2020 will have |year=2020|, |month=January| and |day=(Blank)|.
|startDayOfYear| and |endDayOfYear| will also be present if the range is accurate to days.
Examples:
published event date intepreted eventDate int. year int. month int. day int. sdoy int. edoy 2023-01-13 2023-01-13 2023 1 13 13 13 2023-01 2023-01 2023 1
2023 2023 2023
2023-01-13/2023-01-14 2023-01-13/2023-01-14 2023 1 13 14 2023-01-13/14 2023-01-13/14 2023 1 13 14 2023-01/2023-02 2023-01/2023-02 2023
2023-01/02 2023-01/02 2023
2023/2024 2023/2024
2023-01-01/2023-12-31 2023-01-01/2023-12-31 2023
1 365
Other cases where we can unambiguously determine a date or date range will also be handled, for example a record with a |year| and |month| but no |eventDate|, or non-ISO dates like |January 2023|.
<https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#api-example>
API example:
This record <https://api.gbif.org/v1/occurrence/1234530937> (portal link <https://www.gbif.org/occurrence/1234530937>) is published with |eventDate=2009-03-18/2009-04-13|, |year=2009|, |month=3|, |day=18|. We currently change the |eventDate|:
"year":2009, "month":3, "day":18, "eventDate":"2009-03-18T00:00:00",
With this proposal, we would preserve the |eventDate| but remove |day|, as it the event crosses several days:
"year":2009, "month":3, "eventDate":"2009-03-18/2009-04-13",
This record <https://api.gbif.org/v1/occurrence/2382954724> (portal link <https://www.gbif.org/occurrence/2382954724>) is published with |eventDate=2019-04-06T20:00:00/2019-04-10T05:00:00| and no separate |day|, |month| or |year| values. Currently, we process it to this:
"year":2019, "month":4, "day":6, "eventDate":"2019-04-06T20:00:00",
Instead, we propose returning this:
"year":2019, "month":4, "eventDate":"2019-04-06T20:00:00/2019-04-10T05:00:00", "startDayOfYear":96, "endDayOfYear":100,
<https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#searching>
Searching
The search and download APIs will be affected by this change.
Occurrences will be returned if the occurrence date/date range is *completely within* the query date or date range.
|Search: eventDate=2023-01-11 Record: eventDate=2023-01-11 -- included Record: eventDate=2023-01 -- EXCLUDED Record: eventDate=2023-01-11/12 -- EXCLUDED Search: eventDate=2023-01-11,2023-01-12 Record: eventDate=2023-01-11 -- included Record: eventDate=2023-01 -- EXCLUDED Record: eventDate=2023-01-11/12 -- included Search: eventDate=*,2023-01 (meaning "Before end of January 2023") Record: eventDate=2023-01-11 -- included Record: eventDate=2023-01 -- included Record: eventDate=2023-01-11/12 -- included Search: eventDate=2023-01,2023-01 (meaning "After start of January 2023 AND before end of January 2023") Search: eventDate=2023-01 (same meaning) Record: eventDate=2023-01-11 -- included Record: eventDate=2023-01 -- included Record: eventDate=2023-01-11/12 -- included |
This implementation will avoid returning occurrences with eventDates like "2010/2021" in many queries. (There are millions of occurrences with large ranges like this.)
<https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#density-maps>
Density maps
There is a year filter for the density/pixel maps. An occurrence from 2023-01 will be included, but an occurrence with an eventDate spanning more than a single year (like 2022-13-31/2023-01-01) will no longer be included.
Quarterly analytics, global/regional trends
The quarterly analytics include calculations based on the individual dwc:year, dwc:month and dwc:day fields. The statistics will be affected where these values change or become blank.
<https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#rgbif-pygbif>
rGBIF, PyGBIF
Both libraries will be updated as necessary to support eventDate values containing a date range.
<https://gist.github.com/MattBlissett/ff06599559ce86302a6e84d2e3e605ec#feedback>
Feedback
We have delayed addressing this issue for a long time, primarily due to concerns about changing the existing behaviour of the API. However, it's also one of the most frequently requested improvements to GBIF's interpretation.
If you are aware of software or systems which would have problems adapting to the proposed change, please let us know, either on this mailing list, the GitHub issue, the community forum or by email to me.
We will alert users in the same places when the change is ready to be tested on the test system at api.gbif-uat.org, and when the change is to be made live on api.gbif.org.
Thank you,
Matt
GitHub issue discussion: https://github.com/gbif/gbif-api/issues/4#issuecomment-1385497157
Community forum discussion: https://discourse.gbif.org/t/gbif-api-supporting-ranges-in-occurrence-eventd...
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Adriaan van Os -
Matthew Blissett