Koen et al KNP Diatom Data 2018-2021

[aneriswanepoel]

Diatom report received from Robin Petersen KNP Report_Diatoms 2018- 2021.pdf

@helendallas I am not familiar with this module so perhaps you can take a look first

[helendallas]

First step is to confirm the FBIS Site code for each of these sites. Do this for all sites

Second step is to go to each Site, e.g. X3SABI-LUBYE and click Add algal data

https://testing.healthyrivers.kartoza.com/algae-form/?siteId=9383

Then fill in whatever data you can in this form:

• Sampling dates were either: September of 2018 and 2019, September of 2020 and 2021
• Owner would be Robin I guess?
• Populate the other fields as I have in the screenshot
• Add photos where possible, if available for a site and sampling date. Right click on pdf and save photo. Keep a record in the dropbox folder named photographs.

I dont think anything in this section is in the report, but please check with Philip/Kate re the Autotrophic Index

Then add the taxa recorded, by clicking Add Taxa, select Percentage abundance, click Observed and add abundance value

If a taxon is missing make a note, check with Janette and Kate re algal master list. This should probably be done first to check all species before you start the data capture.

Then add the abiotic data: Table 4: Water quality measured, in situ, during 2018 and 2019. Table 5: Water quality parameter values measured and calculated during 2021. Remember to check the units are correct.

Last Select Source Reference

Work carefully and systematically through the data.

I suggest you first upload one or two to testing to ensure you are comfortable with the process.

[KSnaddon]

@aneriswanepoel is making a list of Algal taxa not on the Master List

[aneriswanepoel]

All data added.. Missing taxa are: Encyonopsis krammeri Brachysira vitrea Cymbella kappii Achnanthidium rivulare Gomphonitzschia ungeri Gomphonema pumilum var. rigidum Anorthoneis dulcis Kolbesia ploenensis Hippodonta Nitzschia dicompressa Rhopalodia operculata Ulnaria nyanse Achnanthidium crassum Navicula vandamii Navicula microlyra Fallacia umpatica Craticula subminuscula Navicula viridula

@helendallas @KSnaddon

[aneriswanepoel]

I've found some more taxa not on FBIS so I've just created a spreadsheet to keep track because the list is getting quite long! Missing algae taxa.xlsx

@KSnaddon

[helendallas]

@KSnaddon Not sure if you added these taxa to the master list?

[helendallas]

No data on FBIS???? Cannot find xls file

https://freshwaterbiodiversity.org/map/#search//taxon=&search=&siteId=&collector=[%22Robin%20Petersen%22]&category=&yearFrom=&yearTo=&months=&boundary=&userBoundary=&referenceCategory=&spatialFilter=&reference=&endemic=&conservationStatus=[]&modules=22&validated=&sourceCollection=[%22fbis%22,%22gbif%22,%22virtual_museum%22]&module=occurrence&ecologicalCategory=&rank=&siteIdOpen=&orderBy=name&polygon=&dst=

[helendallas]

Data found but ownership Ruan Koen. I have emailed Robin Petersen to check. May need to get Janette to correct.

[helendallas]

HD Contacted Ryan Koen and have reassigned correct ownership and uploaded revised pdf from Robin Petersen

[KSnaddon]

@helendallas Am I checking the missing taxa from the KNP diatom data, or are you? I don't think I've looked at the Missing Taxa list before.

[helendallas]

Its all completed and closed

[KSnaddon]

@helendallas There are quite a few not on the ML. I can add these?

[KSnaddon]

@helendallas Sorry I may be missing something. Did you upload a new ML?

[helendallas]

mmm ok, Azeri unfortunately left us hanging here. I have lost track and will need some time to figure things out. please park for now

[helendallas]

No I am. not touching the master list but I don't know what Azeri did with this data before she left and I can't find the xls file either. I need time to figure out what is going on

[KSnaddon]

@helendallas Sure thing, I will leave for now.

[KSnaddon]

@helendallas Just for the record, I checked which ones are not on the June 2023 ML, so you don't need to do that.

[helendallas]

Okay, I think Aneri added data on master list and then left out missing taxa.

@KSnaddon please can you add new taxa that are legitimate. @Janette-Lumley Please can you then add to the algal form directly as described above. I suspect most site visits will exist.

Note Data Owner is Ryan Koen (Not Robin Peterson).

Here are the sites

https://freshwaterbiodiversity.org/map/#search//taxon=&search=&siteId=&collector=[%22Ruan%20Koen%22]&category=&yearFrom=&yearTo=&months=&boundary=&userBoundary=&referenceCategory=&spatialFilter=&reference=&endemic=&conservationStatus=[]&modules=&validated=&sourceCollection=[%22fbis%22,%22gbif%22,%22virtual_museum%22]&module=occurrence&ecologicalCategory=&rank=&siteIdOpen=&orderBy=name&polygon=&dst=&ecosystemType=

This is the study reference

[helendallas]

@KSnaddon @Janette-Lumley Please update me on this ticket

[KSnaddon]

@helendallas I have a relatively short list of taxa to add to the ML. There was an issue last week and I was waiting for Dimas to fix something. I will check later today when I get back to see whether I can add them.

I will then let Janette know which taxa need to be corrected or removed from the spreadsheet.

[KSnaddon]

@helendallas I am still unable to add a taxon manually using "Taxa" on BIMS admin. I need to do it this way, as the GBIF taxa offered to me is either wrong or needs editing. <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

Taxon | Comment -- | -- Snowella | Need to edit the nomenclature on FBIS - change to Snowella Elenkin Achnanthidium crassum | Unable to add to FBIS Brachysira vitrea | Edit on FBIS - synonym Gomphonema vitreum | Added as accepted species of B vitrea Cymbella kappii | Unable to add to FBIS Fallacia umpatica | Unable to add to FBIS Gomphonema pumilum var. rigidum | Unable to add to FBIS - not on GBIF, but is on Algaebase Kolbesia ploenensis | Unable to add to FBIS - Only on GBIF as Kolbesia ploenensis var. ploenensis Nitzschia dicompressa | Unable to add - spelling mistake?? Not on GBIF or Algaebase Ulnaria nyanse | Unable to add - spelling mistake?? Not on GBIF or Algaebase

[helendallas]

@KSnaddon I HAVE ADDED USING WORK AROUNDS, PLEASE CHECK.

Taxon Comment Snowella Need to edit the nomenclature on FBIS - change to Snowella Elenkin - CORRECTED BY FIXING GBIF ID Achnanthidium crassum Unable to add to FBIS - ADDED BY ADDING VARIANT AND THEN EDITING Brachysira vitrea Edit on FBIS - synonym - REVISED AND ADDED GBIF ID Gomphonema vitreum Added as accepted species of B vitrea Cymbella kappii Unable to add to FBIS - ADDED BY ADDING VARIANT AND THEN EDITING. THIS IS A SYNONYM OF Cymbella kappii (Cholnoky) Cholnoky, 1956 Fallacia umpatica Unable to add to FBIS - ADDED AND ADDED GIBIF ID SYNONYM Gomphonema pumilum var. rigidum Unable to add to FBIS - not on GBIF, but is on Algaebase ADDED - NEED TO SELECT FAMILY FROM LIST Kolbesia ploenensis Unable to add to FBIS - Only on GBIF as Kolbesia ploenensis var. ploenensis ADDED BY ADDING VARIANT AND THEN EDITING. Nitzschia dicompressa Unable to add - spelling mistake?? Not on GBIF or Algaebase ADDED NOW Ulnaria nyanse Unable to add - spelling mistake?? Not on GBIF or Algaebase NOT DONE YET

[KSnaddon]

@helendallas Cymbella kappii is a species and not a variety, as far as I can see. I have edited it to be species but just checking to see whether this is correct? C kappii is a synonym of C turgidula

Cymbella kappii Unable to add to FBIS - ADDED BY ADDING VARIANT AND THEN EDITING. THIS IS A SYNONYM OF Cymbella kappii (Cholnoky) Cholnoky, 1956

[KSnaddon]

@helendallas For this one - I changed it from a species to a variety and corrected the scientific name to the one provided on Algaebase.

Gomphonema pumilum var. rigidum Unable to add to FBIS - not on GBIF, but is on Algaebase ADDED - NEED TO SELECT FAMILY FROM LIST

[KSnaddon]

@helendallas Found this on GBIF as a synonym so changed from species to synonym on FBIS. Also added the accepted species

Kolbesia ploenensis Unable to add to FBIS - Only on GBIF as Kolbesia ploenensis var. ploenensis ADDED BY ADDING VARIANT AND THEN EDITING.

N dicompressa doesn't appear anywhere but happy that you've added it so that we can upload the data!

Nitzschia dicompressa Unable to add - spelling mistake?? Not on GBIF or Algaebase ADDED NOW

Added Ulnaria nyanse

[KSnaddon]

@helendallas This dataset needs one more cross-check with the ML, and then it's ready for upload

[KSnaddon]

@helendallas @Janette-Lumley Do you want to send me the occurrence data spreadsheet for a last check? I don't think any of the data need to be deleted as we have added all the taxa?

[Janette-Lumley]

@KSnaddon I wasn't involved in capturing this data. Looking at this ticket from the beginning I assume that Aneri captured this data mannually into FBIS. @helendallas do I need to capture the ones that were missing as per Aneri's excel file above and have they all been entered into the master list?

[KSnaddon]

@Janette-Lumley Helen and I have added the ones that were missing off the Master List, so if we assume the list of missing taxa that Aneri put together is the full list, then all should be OK for upload.

[helendallas]

@Janette-Lumley Plase can you contact Azeri and check. I am not sure what she did here / or check taxa against the report.

[helendallas]

@Janette-Lumley Please update me on this ticket soonest. Thanks

[Janette-Lumley]

@helendallas Aneri captured this data manually into FBIS as at the time there was no upload template for algae. She left out the ones that weren't on the master list. I have captured the missing ones now in the upload template. Attached here and added to the Janette Only folder on dropbox. There is just one missing from the master list now. It is Ulnaria nyanse. Koen et al Water Quality Report_Diatoms_KNP Missing data.xlsx

[helendallas]

@Janette-Lumley Thanks. DO you know how to add a taxon onto FBIS but selecting the site and editing the data....it's quite easy and will be better than uploading because of issues with making new erroneous site codes which I am still trying to resolve with Dimas

[Janette-Lumley]

@helendallas ok I will add the data into FBIS, I did start like that but the system kept hanging so it was taking very long. I will try again.

[helendallas]

actually lets leave it. O am not happy with the data as it has been labelled frustule count??? not Sur eif that is correct.

I would prefer to delete the data on FBIS and for to add you xls data to the file I have downloaded. I will send shortly. Thanks

[KSnaddon]

@helendallas What is the issue with Frustule count? Can I also see the spreadsheet?

[helendallas]

@Janette-Lumley I managed to download the Koen data Aneri added to FBIS. Attached. Please can you add your missing data file to this making sure that the final combined file has all the taxa listed in the original report with correct information. Thanks

@KSnaddon Please can you check what the correct Abundance measure is. Aneri has used a mix of frustule count and percentage. My knowledge of algae is suspect, so would appreciate guidance on the correct measure.

Once completed, please send to me for a final check. I will then delete the current Koen study on FBIS and we can upload the new datafile.

Koen et al Kruger Algae from FBIS.xlsx

[KSnaddon]

Will do @helendallas

[KSnaddon]

@helendallas The KNP diatom data are recorded in the original report as both a count and a %. The units for the count are not recorded, and it's unclear from the methods. If I have to guess it may be a count per 400 ul. However, it may be the best plan to just add % or proportion as an option for algal data?

[KSnaddon]

@Janette-Lumley has now checked the data as entered, and they have been entered correctly but should all be %.

[Janette-Lumley]

@helendallas and @KSnaddon here is the updated spreadsheet, I have added the missing taxa.

Koen.et.al.Kruger.Algae.from.FBIS.xlsx

[Janette-Lumley]

@helendallas and @KSnaddon don't use the above spreadsheet, I am just fixing up some of the original data so I will send the final one as soon as I am finished. Thanks

[Janette-Lumley]

@helendallas and @KSnaddon These are the final spreadsheets, I have entered the data into the latest upload template and also to the file you downloaded from FBIS Helen. I am not sure which is best to use for uploading the data. Koen.et.al.Kruger.Algae.from.FBIS.xlsx Koen.et.al.Kruger.Algae.Final.xlsx

[KSnaddon]

@helendallas Let me know when we can sit together and do the various uploads?

[helendallas]

@helendallas Doing final check and edits . Old data needs to be deleted first. then new excel file uploaded

[helendallas]

@KSnaddon I uploaded this to testing but one taxon is still missing

Ulnaria nyanse

[KSnaddon]

@helendallas LOL - I had added that species to the Fish module by mistake a few weeks back! I kept on wondering why I couldn't find it in Algae. I have corrected that now.

[helendallas]

ha ha

[helendallas]

@KSnaddon Please can you add it to testing as well as I need to upload it there first so Janette can check.

[KSnaddon]

@helendallas Done

[helendallas]

@helendallas Needs to check what Koen sites are already on FBIS with this data. May be best to just stick to same sites as created by Aneri and to re upload the data to these sites