Help Documents

For New Users & Group Settings

Leachman help doc for volunteers

Siobhan Leachman. (2020, June 26). Auckland Museum Volunteer Instructions for Bionomia. Zenodo. 26pp. PDF

Focused Tasks

Scribe Siobhan Leachman (see her Twitter feed) also produced a helpful series of step-by-step tweet threads. These are reworked with minor edits as focused tasks below.

Getting Started with ORCID & Claiming Specimen Records

First, you need to get an ORCID identifier. This is because you'll be creating and adding data to the site. So, if you do not have an ORCID, got to and get one. Please make some information you put into ORCID public such as your employer or add one of your publications. This ensures that someone will know who you are. See the Get Started page to learn what public details Bionomia draws-in from your ORCID account.

Then, login to Bionomia using your ORCID account. You will first be taken to the Overview page in your profile. If you have collected specimens whose metadata has been loaded into GBIF, you can go to the Specimens tab to claim them. profile tabs

This will link your specimens to your ORCID identifier, enriching the data and helping to ensure you get credit for your work at collecting or identifying specimens. Claim your specimens by pressing the net button for those you have collected, the microscope button for those you have identified, or the Both button where you have done both. If you did not collect or identify a candidate record that Bionomia found, click the Not me button.

Specimen claiming buttons Not me buttons

Don't panic if you make an error! You can rectify it. Go to the Claimed subtab to adjust the records you indicated as identified, collected or both. Go to the Ignored subtab to reclaim the records you indicated as "Not me".

Once you have claimed your specimen records, press the Science Enabled tab. This will show you what papers have used your specimen records in their analyses. This relies on the authors of those papers crediting and citing the download DOI of the GBIF dataset they used.

Visit Setting & Integrations to make your Bionomia profile publicly available. Settings & Integrations Make profile public

Helping Others

So I'm going to start by choosing someone to help. I've logged into Bionomia with my ORCID id & I've pressed Help Others button on the top right. I'm now going to pick a country. Yep, New Zealand! I'm going to pick the entomologist George Howes.

Help Others button Countries helping list Help New Zealand George Howes

The reason I've chosen him is that I started his Wikipedia article. I think he was marvellous and should get credit for his collecting work. His Bionomia page looks like this. George Howes The first specimen was collected by someone with his initials, at the correct dates, is held in a New Zealand collection. I'm confident he collected it. So, I press the net button beside the specimen. Selecting P. fenwicki If I was confident he had collected ALL 25 specimens in this view, I could have pressed the white net with black background. That would automatically attribute to him in bulk all these 25 specimen records (but no more). I can even increase the number of specimens on the page up to 250 (bottom-left dropdown) and bulk assign all of them!

Bulk assignment buttons Per page dropdown

But in this case some way down the set there are specimens collected by "G Howes" in NHMUK. I'm unsure whether this is OUR George Howes. If I'm unsure it is him or not I'll have to leave the specimens. Helping unsure To try and work out whether it is George I'll click on the scientific name on the specimen. This opens a new tab & takes me to its details in GBIF. Here I can see it's a specimen from the Leith Valley in Dunedin, collected in 1922 by G. Howes. Helping GBIF Yep it's our George! So I'll claim those specimens for him.

BUT you still have to be very careful. I keep an eye on dates. On the next page I see a page that isn't 1921 or 1922. There's a specimen collected in 1937 - still while our George was alive. But again dates - so I click to check. That specimen WASN'T collected by George. It was collected in Bolivia. parvispina 1937 parvispina 1937

Further down I see specimens coming from FishBase, but George was an entomologist. I confirm that he didn't collect those specimens either. So I claim the specimens he did collect and press the Not them button for the one's he didn't collect or identify. parvispina 1937

Creating a Wikidata Item

Once you've mastered the art of attributing specimens in Bionomia you may want to try to get more challenging collectors like Miss Blackler into Bionomia. This is my favourite area of work as it's like a detective hunt. And I've got lots of friends to help!

I came across "Miss Blackler" as I had seen her in the @HarvardHerbaria Index of Botanists. She collected in Oregon and California. I created a @Wikidata item for her and added the HUH identifier.

Harvard Index of Botanists Wikidata screen capture

But to add her to Bionomia I need to get a date of death. And that's where it can get tricky. Our Miss Blackler collected in Olympia and @metacoretechs found a reference to a Lydia Hooper Blackler in the Internet Archive. Blackler Internet Archive

Based on info @idbdeb found, Lydia Hooper Blackler lived in Olympia, remained unmarried, travelled & lived in California, where other specimens of hers were collected, As a result I'm confident that this is our "Miss Blackler". She's also in @FindaGrave. Find a Grave So now I update her Wikidata item. I'll add as much information as we've found, add as many references as I can so that other researchers can track what we've done. I'll include the important date of death. Wikidata date of death I've also found a public domain image of her via @OrHist Before I add her to Bionomia I'll download this and upload it to @Wikicommons. I can then add it to her Wikidata item. This in turn will be pulled into Bionomia when I add her to the site. Photo of Blackler

Now I add her to Bionomia. I take her Wikidata item Q93018256 and go to the site. I press the Help Others button top right, and then the Add Someone tab. I add the Wikidata Q item number in and press the green Add button.

Help others link Helping tabs Add someone

She's then added to Bionomia, it's just a matter of clicking on her and then attributing specimens like we did previously for George Howes. Helping Blackler Don't forget to press Make Public ...once you've attributed a few specimens. You don't HAVE to get to 100%, anything is better than nothing.

Uploads to Attribute Records in Bulk

Today I thought I'd share a "how to" for bulk uploads. After only a day of doing these I feel like I need the extra practise. Plus some other folk have mentioned they'd like to join me in attempting this but don't know how. So here it goes!

First you have to find a person with specimens that need uploading. I'm going to pick the fabulous Alexander Wetmore. I've previously transcribed his photo albums with @TranscribeSI. He was a prolific collector and needs some @BionomiaTrack love.

Wetmore overview

So I go to the "Bulk Attributions" tab on his profile page. And then press the blue "Download" csv file button.

Wetmore download Download buttons

This downloads a csv file of specimen data. I open up the file. Now I'm going to be using Excel but you may use something else. When opened the file looks like this in Excel.

Excel download

I'll go through the important columns. The first is the "action" column. This is where you'll put "recorded" if the specimen was collected by Alexander, or "identified" if it was identified by him. If he did both you add "recorded, identified". Note the comma separating the two!

recorded identified

You can see whether Alexander recorded or identified specimens by checked the "recordedBy" or "identifiedBy" columns in the spreadsheet.

recordedBy identifiedBy

The other column that may be of use is the "Not Me" column. If it isn't your collector that either collected or identified the specimen you can add "True" to this column.

Not me

Once you've got your spreadsheet ready with some claims added you can then upload it into Bionomia. I'm just going to do a few so I can show you what to do. I'm going to assume you have basic Excel skills. All I'm going to do is use the sort & filter and search recordedBy.

Sort and filter

I'll add "recorded" in the "action" column to all those lines. I'll then check the "identifiedBy" column to make sure he didn't identify any of the specimens. If he did I'll add a comma and "identified" to those specimens he also identified.

Adding action

Now obviously you can keep on working on the spreadsheet. But I'll just leave it there so I can show you the next steps. What I do next may not be the best way but it works. I save the spreadsheet and a warning pops up. I press "No" on the warning and save as an Excel workbook.

CSV dialog Saving csv as workbook

I then press "save as" and choose the file format CSV UTF-8 format. I'll rename the file as Q34558Alex.csv.

Save as UTF-8

Then I go back to Bionomia - Alexander's profile, the Bulk Attributions tab and press "Choose file". I choose the file I've just renamed and saved as a csv file. Then I press submit.

And the 56 records that I've done will be added. The biggest batch you can do is 10,000. So there you go and happy bulk uploading of data!

More on Wikidata

Leachman, S., & Mabry, M. E. 2024. Integrating Wikidata with Data Sleuthing Techniques For Enhanced Knowledge Discovery of Hidden Figures. Zenodo.

Leachman, S., & Mabry, M. 2024. Tools and Resources for using Wikidata. Zenodo.