Content comments for biorepo portal redesign

[kyule]

Brackets indicate suggested additions, deletions, or edits to text.

• About samples page: The NEON Biorepository publishes occurrence records for every archived sample and specimen, as well as additional value-added sample-associated data not present in NEON data products [in the sample portal] and makes these samples available for loan.
• Sample Repositories page: (1) I noticed a couple instances without a comma before the "and" at the end of a list... I personally have a semi-strong preference that those be included. Nitpicky but it slows down my comprehension of a sentence. (2) Part about LMZ: At least historically, this is not the only pathogen testing lab (and it's not mentioned that they test other things) so I think it's awkward to include here unless NEON really wants to. (3) All tick voucher specimens collected by NEON during construction and continuing through [field year 2023] are available and will be curated through the U.S. National Tick Collection at Georgia Southern University. [All tick genomic extracts and tick specimens collected in 2024 and beyond are available from the NEON Biorepository.] (4) Megapit samples.... odd because only the distributed initial characterization samples are in MI. The megapit samples are actually at NEON HQ and will move to ASU after renovations... (5) Assignable Assets --> Research Support Services (6) "previously collected in Florida" --> previous to what? I think 2018 but idk (7) MSB is duplicated in the list (8) Carnegie/Essig, super not a true statement, I would update to just 'taxonomic reference specimen collections' (9) Questions about samples not housed at the NEON Biorepository at [Arizona State University] should be sent directly to those repositories. --> i.e. replace the part "to the NEON Archival Samples Team." .. I think that form is dead or at least the link doesn't work (10) Hawaii - move to the above section and specify it's only voucher specimens collected prior to ~2023
• Sample services page: (1) [Loans of e]ndangered taxa, fragile specimens, or samples which are deemed to be in limited supply [may be subject to more stringent review]. (2) Assignable Assets --> Research Support Services and link
• Dataset publishing page: (1) Published Research Dataset --> Goes to "old" page format and seemingly Has not been integrated yet Can we bundle with checklists like "Research Datasets and Checklists"? (2) Delete this: These sample lists will be published to the Environmental Data Initiative portal, increasing the visibility of sample use in researhc. (3) such as the Global Biodiversity Information Facility (GBIF) portal[,] further increasing their visibility to the broader research community.
• Sample analysis page: (1) Rest API explorer link not active (2) [To track samples moving between facilities, ]NEON generates shipment manifests and standardized receipt forms that enable NEON to track the location of a sample through its lifetime from generation in the field to final disposition. (3) Screenshot from the sample explorer actually doesn't have any shipment or location data displayed because it represents the tagged mammal and not any samples, so that is a bit confusing in the context of the above text IMO
• Checklists page: I know you know but this is the one super obvious place images need to be switched.
• Search results page: (1) "Occurrence Records" tab easily gets cut off depending on the window size (2) recommend a note saying the number of images at the top like is done on the species list tab especially since if there are none since it seems like the page just isn't loading or something (3) maybe known issue for some other reason, but the maps don't load
• Main landing page: Not sure where those stats come from, since some are not correct (species count, years, and probably images)
• Maybe I missed it, but IMO Symbiota and BioKIC homepages should be linked somewhere
• Will the management tools and sitemap etc show up when we are able to log in? Will they essentially look the same as before?

[sunray1]

Will the management tools and sitemap etc show up when we are able to log in? Will they essentially look the same as before?

https://biokic4.rc.asu.edu/neon/portal/profile/index.php

You can log in here using the Symbiota log in for now - I commented some unused tools out but everything is basically the same

[sunray1]

(3) maybe known issue for some other reason, but the maps don't load

Yup, maps won't load since biokic4.rc.asu.edu is not the associated domain for the maps - should be fine once it is switched to biorepo.neonscience.org

[sunray1]

(1) "Occurrence Records" tab easily gets cut off depending on the window size

Do you mean like this?

[sunray1]

I also note a weird behavior where the image tabs and occurrence records tabs are not switching independently of each other.

https://biokic4.rc.asu.edu/neon/portal/collections/search.php?taxontype=2&usethes=1&imagecount=all&submitaction=search&page=2

[sunray1]

Main landing page: Not sure where those stats come from, since some are not correct (species count, years, and probably images)

I mostly grab these with SQL - I wrote real simple queries for them, but you would know better what they should be:

• Species Count: SELECT COUNT(DISTINCT(sciname)) FROM omoccurrences;
• Record Count: SELECT COUNT(*) FROM omoccurrences;
• Image Count: SELECT COUNT(*) FROM images;
• Years: Current Year - 2020
• Sample Types: hardcoded as 20
• Sites: hardcoded as 81

[kyule]

(1) "Occurrence Records" tab easily gets cut off depending on the window size

Do you mean like this?

Yep, exactly!

[sunray1]

Maybe I missed it, but IMO Symbiota and BioKIC homepages should be linked somewhere

whoops - made the logos in the footer clickable

[kyule]

Main landing page: Not sure where those stats come from, since some are not correct (species count, years, and probably images)

I mostly grab these with SQL - I wrote real simple queries for them, but you would know better what they should be:

• Species Count: SELECT COUNT(DISTINCT(sciname)) FROM omoccurrences;
• Record Count: SELECT COUNT(*) FROM omoccurrences;
• Image Count: SELECT COUNT(*) FROM images;
• Years: Current Year - 2020
• Sample Types: hardcoded as 20
• Sites: hardcoded as 81

Got it. Is this linked to an older version of the database that still has the external portals? That would actually explain a lot. Either way, I would change images to SELECT * FROM images WHERE occid IS NOT NULL;

Years is debatable, but full operations began in 2019, so needs to be at least 5. I'd argue for advertising a longer series, since we have some full protocol x site sample sets dating back to 2014.

[sunray1]

Got it. Is this linked to an older version of the database that still has the external portals?

Yeah - I think it's linked to a version from May