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can you see where this can be added in the OBIS manual?
https://obishq.slack.com/archives/CV2RM44KW/p1664452286825799?thread_ts=1664394922.788529&cid=CV2RM44KW

Related:
iobis/quality-taskteam#7

https://manual.obis.org/examples.html

The recommendation for occurrenceID should be a URN or LSID, see DwC definition and https://www.labkey.org/Documentation/wiki-page.view?name=lsidOverview

Hello,

The link to Examples: ENV-DATA and DNA derived data from the specific sentence below at this page: https://manual.obis.org/data_format.html#edna-dna-derived-data-extension returns page not found.

Refer to the Examples: ENV-DATA and DNA derived data for use case examples of eDNA and DNA derived data.

Thanks a lot!!

Options for page width to avoid scrolling in tables
https://manual.obis.org/examples.html

It would be interesting to have Python code at least for the main parts of the manual.

The manual is now published to GitHub pages at https://iobis.github.io/manual/, but a number of items still need to be fixed, including missing page titles.

Hi,
The reader has no idea which DwC terms will remain as information once harvested by OBIS, and which will remain only when the suer downloads the original DwC-A file.

Thank you.

There is an error in the item 3.5 (https://manual-dev.obis.org/identifiers.html): the eventID title is not showing correctly. Probably you need to jump one line.

Update the:

• examples page and
• the page for imaging data

with guidelines from “Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures.” [http://dx.doi.org/10.25607/OBP-1742]

I converted the manual to bookdown in https://github.com/iobis/manual/tree/book, but there are many loose ends including internal links and within-page tables of contents not working. Custom anchor links can be removed as bookdown generates them automatically for each (sub)heading. We also have to check if no pages have been left out of the new structure.

@EliLawrence In case you want to work a bit on this, the sequence of files is defined in _bookdown.yml.

Also to do: set up GitHub action.

Current eventType DwC guidelines https://dwc.tdwg.org/terms/#dwc:eventType
In the Manual we currently suggest type or eventType. I think it would be good to provide some more guidance on which kinds of standard vocab could be used to fill this field.
Happy to hear any suggestions

• On section 3: the phrase "At this step, there are different non arbitrary you need to do with your data, but it is important to determine which structure best suits your dataset before proceeding." sounds a little bit strange for me. Maybe rephrase?
• 4.2.1.4 Step 2: Match with other registers: it's a bit confusing, because at first we say that we only accept three authorities (WORMS, NCBI and BOLD).
• 4.2.3 Taxon Match Tools Overview: on table, where is "Outputs a tibble for each taxa name specified, Requires knowledge of R or python", change comma for a new line or ';'.
• 4.5.1: convert note (*For measurementTypeID, measurementUnitID, and measurementValueID you must use controlled ...) into a quote format (using >).
• 4.8: suggestion - change 'Contents:' for some introductory phrase, e.g.: "When formatting data for submission on OBIS, some of the common problems you may find are: [then the list]"
• 4.8 times/dates: convert"A note about intervals..." to quoted format (with >)

The videos are great!

Will be great if there is a section in the OBIS manual that shows the recommended fields for extensions (e.g. DNA derived data extension) where we want to encourage data provider to fill in because OBIS/GBIF (or others) are building tools based on these fields

Example use case:
DNA_Sequence field

• iobis/quality-taskteam#36 (comment)
• iobis/quality-taskteam#36 (comment)

According to Darwin Core Terms descriptions in https://dwc.tdwg.org/list/#dwc_identificationQualifier the following example should be:

Take an example specimen named Pterois cf. volitans. The associated occurrence record would have the following taxonomic information:

scientificName = Pterois
identificationQualifier = cf. volitans (delete volitans, here you use only cf.)
specificEpithet = leave blank (fill in with volitans)
scientificNameID = the one for Pterois
taxonRank = genus

This example is in this section of the OBIS manual: https://manual.obis.org/common_qc.html (5.6.6 Low confidence taxonomic identification).

I am continuing an ongoing conversation with @pieterprovoost and @ayushanand18 here. To summarize discussion so far:

• The OBIS API documentation is comprised of:
  • the swagger endpoint api.obis.org
  • robis & pybobis docs
  • this manual

I have the following suggestions:

1. pagination of results from the API should probably be explained a bit.
2. a short note on how the usage of hasextensions might exclude a lot of results might be helpful.

I will suggest changes to address these once I have the extant swagger file(s).

Section 1.4: https://manual-dev.obis.org/gethelp.html#getting-help-in-obis
OBIS Website resolves to 'page not found'

Currently GBIF don't inherit from parent events for occurrence data.

If parentEvent contains lat/lon and child events leave them blank (inheritance), the occurrences associated with the child events will have empty lat/lon. These fields are not currently populated by GBIF.

Will be great to have a section in the manual for this so that the data will be useful for both GBIF and OBIS :)

According to this GBIF discourse https://discourse.gbif.org/t/a-nbsp-mystery/4315 I think it would be useful to add this to our QC recommendations

https://biss.pensoft.net/article/38084/element/4/4784354/

As we have received no comments on the suggestion at iobis/obis-issues#212, align the recommendation for scientificName with https://dwc.tdwg.org/list/#dwc_scientificName.

• Link to the robis demo list
• Move the data access info from the website to the manual

E.g.
Occurrence (Core/Extension)
x/x
/x
x/

So we can easily distinguish between terms for the Occ core vs Occ extension tables. Would help clear up confusion

Remove numbering
Fix typos

Document the use of geometries, specifically from mregions/mregions2 with robis, including simplification or bounding box + local filtering.

In this section: https://manual.obis.org/common_formatissues.html#missing-required-fields

The last link in this sentence needs to be updated, because it doesn't resolve to a specific heading:

You can use the Marine Regions gazetteer to search for your region of interest and obtain midpoint coordinates. Guidelines for using this tool and for dealing with uncertain geolocations can be found here.

I think it's intended to link to this section: https://manual.obis.org/common_qc.html#uncertain-geolocation

Elizabeth asked me to put my feedback in one issue. Sorry I don't have time to do a PR right now, but I can pitch in later if time is short for y'all too.

1. section 1.5 3.
   • Typo in section header: 'Frequency' should be changed to 'Frequently'
2. section 1.5.0.4
   • incorrect link: What are the OBIS quality control flags?
   • update to: https://manual-dev.obis.org/dataquality.html
3. section 1.5.0.6
   • incorrect link: How do I contact the data provider?
   • update link to: https://manual-dev.obis.org/access.html#how-to-contact-data-provider
4. section 2
   • bad link format: "run a series of quality control measures"
   • replace '.md' with '.html'
5. section 2.1
   • bad link: "Data from OBIS is accessible in numerous ways[LINK to access section] "
   • needs link
6. section 2.1:
   • bad link format: "Your dataset can be associated with a DOI"
   • needs link
7. section 2.3
   • bad link format: "moved into the extendedMeasurementOrFact table"
   • needs link
8. section 2.4.1.1
   • link to "Darwin Core" lands on web page that isn't very friendly to new users (http://rs.tdwg.org/dwc/)
   • replace with: https://dwc.tdwg.org/
9. section 2.4.1.1
   • link to OBIS xsd resolves to general OBIS website: "an OBIS extension"
   • needs updated link
10. section 2.4.1.3.1
    • misspelling
    • correct AlphiaID to AphiaID
11. section 2.4.1.3.1
    • misspelling
    • correct belowe to below
12. Section 2.4.1.3.1 misspelling
    • 'NO'should be corrected to 'ON' in "The use and definitions for additional NO signs"
13. section 2.4.1.3.3
    • dissonant guidance with GBIF DNA publishing guide
    • "or MachineObservation (e.g. for occurrences based on automated sensors such as DNA sequencers, image recognition etc)."
    • but DNA publishing guide says use 'MaterialSample'
    • also occurs in section 4.8.1
14. section 2.4.2.2.3
    • Duncan et al. (2021) resolves to ambiguous search results (or at least I was expecting a single document).
    • other occurences throughout the manual
15. section 2.4.4
    • link resolves to generic page: "See more information on EML."
    • need to update link
16. section 2.4.4
    • link resolves to obis homepage: "Also read the guidelines on the sharing and use of data in OBIS."
    • update link
17. section 4.6.1
    • incorrect link: "will occur within the extendedMeasurementOrFact extension."
    • need to update link
18. section 4.8.2.1
    • broken link: "The Data Carpentries have produced this exercise"
    • need to update link
19. section 4.8.4.2.3
    • duplication of the word 'here'
20. section 4.9.1.2.1
    • broken link due to domain change: “18S Monterey Bay Time Series: an eDNA data set from Monterey Bay, California, including years 2006, 2013 - 2016
    • update to: https://ipt-obis.gbif.us/resource?r=18s_monterey_bay_time_series_edna
21. section 4.9.1.3.2
    • subsection 'content' seems like it's just links to the next three subesctions? Not sure of it's function.
22. section 5.3
    • broken link: "As you are following the guidelines in this manual to format data"
    • need to update link
23. section 5.4
    • bad link format: "this MoF statistics report https://r.obis.org/mof/""
    • remove " from link
24. section 5.6.2
    • bad link format: For information on how to use this tool, see below.
    • need to update link
25. section 6.2.3.
    • in several places there are links to the outdated manual wiki
    • update IPT manual link to: https://ipt.gbif.org/manual/

Putting this here as part of the suggestions received from node manager

We have noticed an issue with the GBIF documentation that points to OBIS regarding the namespace for ExtendedMeasurementOrFact. The following link in the GBIF documentation does not resolve:

http://rs.iobis.org/obis/terms/ExtendedMeasurementOrFact

We (DiSSCo/opends) are interested in using the ExtendedMeasurementOrFact extension in our data schema, but the unresolved link and unclear namespace management are creating uncertainty. We need to ensure that we are referencing the correct and maintained namespace to avoid issues in our implementation.

On section 4 - Formatting data tables - add a page showing how to use the obisdi package for data formatting and ingestion in a standardised way. The package is under development, but already with good stability. Soon a new update will be posted with minor improvements.

The seagrass example at https://manual.obis.org/examples.html#seagrass-cover-and-composition has POLYGON with two points, this needs to be four at least (so it's closed).

Suggest to update practices in the following section into the one mentioned by @albenson-usgs in gbif/pipelines#217 (comment)

Current wordings can be improved: gbif/pipelines#217 (comment)

Page: https://manual-dev.obis.org/darwin_core.html#taxonomy-and-identification

2.4.1.3.1 Taxonomy and identification

scientificName (required term) should always contain the originally recorded scientific name, even if the name is currently a synonym. This is necessary to be able to track back records to the original dataset.

Hey,

We are updating our data publication wiki and would like to cite the OBIS manual as we referenced the material from the manual. Is there a preferred way to cite this?

For example - suggested citation for GBIF's best practice guide in publishing sampling event data

GBIF (2018) Best Practices in Publishing Sampling-event data, version 2.2. Copenhagen: GBIF Secretariat. https://ipt.gbif.org/manual/en/ipt/3.0/best-practices-sampling-event-data

Provide some guidence on working with mixed ISO 8601 date formats in R, Python, and Excel as part of the "using OBIS data" section.

See https://postgis.net/docs/ST_PointOnSurface.html

This does not appear to be working with depth more than 2:

bookdown::gitbook:
    toc_depth: 3

In the depth figure (section 2.4.1.3.4 in the OBIS Manual): looking at scenario 4 - should the reference point be at the sea surface (elevation) level, with the top of the trawl being the minimumDepthInMeters sampled, and the bottom end of the trawl perhaps indicating the maximumDepthInMeters?

If not, could someone perhaps explain how scenario is included in the event core? Seems like there'd be 2 values for minimumDepthInMeters associated with a single event?

Users are unclear about current QC done by OBIS, possibility to document the qc process in manual?

Related:

• iobis/quality-taskteam#18
• iobis/obis-issues#182
• iobis/obis-issues#180

Move all documentation to vignettes under https://iobis.github.io/robis/