Asia Office Hours

[cjk]

Today @vijay.barve, @Lily, @melissa0520 and I started the Asia Office Hour as a casual space for BIFA teams to have LIVE Q&A sessions on (mainly) data publishing.

For our first session, I prepared a flowchart trying to answer the qualification part of the most frequently asked question: How to publish data with GBIF?

Yes, that question needs a four-day workshop to cover properly, but in the office hours we will fill gaps, speaking in other words and hope some live interactions will improve knowledge retention.

I shared this slide with participants today. Hope it’s self-explaining! Please comment if you find anything incorrect or unclear, so I can revise it.

[cjk]

Thanks again for those who joined today! Special thanks to Choki from Bhutan for sharing the biodiversity information portal for Bhutan, and it’s role in supporting domestic citizen science activities. We also learned how the data underneath have been published to GBIF.

The same software stack was also used for India Biodiversity Portal. They look really nice indeed!

[vijay.barve]

In the recent edition of Asia Office Hours, we discussed about

• Geocoding historical data where GPS coordinates are not available. Need for carefully assigning the coordinate uncertainty values.
• How google maps can be used to get locations and uncertainty
• What exactly is occurrence status and how absent can be used
• Can a publisher use multiple IPTs to publish different datasets.

[melissa0520]

Recommended IPTs for Asia region if there are no IPTs hosted in your node or institution:

• Asia regional IPT: https://cloud.gbif.org/asia// Contact: asia_support@gbif.org

• TaiBIF IPT (Taiwan node): https://ipt.taibif.tw// Contact: taibif.brcas@gmail.com

[melissa0520]

From the Asia Office Hour last week, we discussed about

• The best way to georeference several locations at once

Geocoding API 1
Geocoding API 2

• The best practices for using DwC terms
  • remember to add the information in “acceptedNameUsageID” about what taxon and the specie taxon ID you refer to (i.e. Species2000, Catalogue Of Life)
  • recommend accepted specie name resolver: Global Names Resolver
  • how to do if there is no any date information of specimens: should provide the date/year range than a blank. i.e. 2007-03/09, 2007-05-20/25, 1900/1909 (some time during the interval between the beginning of the year 1900 and the end of the year 1909)

Welcome to join us every Thursday or keep following the posts here!

[cjk]

How to convert “day, month, year” columns into ISO 8601 yyyy-mm-dd format in Excel?

[cjk]

Thanks to Dr Lu, Dr Pujary and Riya for joining us today! We enjoyed having the opportunity to elaborate about the structure of Darwin Core Archive, GBIF data connection with citizen science activities, the value of having a GBIF data publishing badge and how to meeting the data publishing requirement for BIFA midterm report. It was also good to explain about why GBIF only allows institutions to be data publishers. Hope you find it useful, too!

[melissa0520]

Since there are more and more DNA barcoding data in biodiversity research, here are some suggestions for DNA-related data publishing:

• Use this term if the sequence is already publish to NCBI : http://rs.tdwg.org/dwc/terms/associatedSequences

• If it is eDNA, it would be different and you can choose extension to provide the data:
  https://rs.gbif.org/extensions.html
  

• DNA derived data extension: https://rs.gbif.org/extension/gbif/1.0/dna_derived_data_2022-02-23.xml

• DNA data publishing guideline: https://docs.gbif.org/publishing-dna-derived-data/1.0/en/publishing-dna-derived-data-through-biodiversity-data-platforms.en.pdf

[cjk]

Thanks to the participants today. It’s great to learn about the efforts from Botanical Survey of India that has herbaria resources catalogued. NGCPR is another CSR contribution from India that awaits further engagement with GBIF data publishing and domestic conservation experts. Hope we will hear more from them.

For those who are busy preparing the first dataset for the midterm, if you find no clues about certain fields not showing up, we have a hint for you. On your dataset page at GBIF.org, look for “DOWNLOAD” tab near the title, and choose “GBIF annotated archive”:

And then once you’re logged in, choose “DARWIN CORE ARCHIVE” and wait for the notification when it’s ready.

What you will download is what GBIF.org sees as the result of your data publication. Therefore, by examining the text files, you may be able to spot the missing part, for example, wrong mapping, when you discovered that the header in the CSV file doesn’t represent the value in the same column.

But don’t forget, depending on the scale of the potential issue, sometimes it’s still easier to see the comparison if you examine each occurrence record. There you have the “Interpreted” VS “Original” to understand how your dataset has been, eh, interpreted.