tigerhawkvok / asm-mammal-database Goto Github PK

Right now it looks like only the Genus and Species are searchable on the main page? When I type in Rodentia or Muridae I get no search results. Ideally a user would be able to type in anything in the database, e.g., "Thomas" to get all the mammals that Thomas described, etc. -- would that considerably slow down the searches?

When attempting to download my search results I encountered two separate problems:

1. I tried several different searches of various sizes, but the HTML/PDF option nearly always failed (an exception is that the HTML option worked but not the pdf for Ursus arctos). A popup appears briefly which says "Failed to create file", but then the "Select Download Type" popup box remains up and I couldn't get it to disappear unless I refreshed the page.

2. The CSV download option worked great, but I noticed one odd thing: If I clicked a search result to see the info on a particular species, selecting download from that species' page provides the option to "Use current search results", but turning that on didn't restrict the download. The download worked, but I got the whole database. Not a big problem, but having the option for the just the current search results made me think it was somehow able to tap into the search results that led me to the page I was on (of a single species) while downloading. If this is unavoidable, perhaps a simple notification somewhere would help clarify?

When on the About or Summary pages its not easy to navigate back to the main search page, other than to just hit the browser back button. So can we make the ASM logo on the left be associated with the text "Home", and then have it redirect to mammaldiversity.org? I think we don't need to have a direct link to the ASM website other than on the About page.

Thanks!

pretty and csv, like SSAR

Lets go with text + icon for the header bar, so that it jumps out at folks more easily to start with. So it would be:

About + icon
Statistics + icon
Forum + icon
Random species + icon

I'd be fine with following that through the entire website, or if its easier we could have icons-only on all pages other than the front page

Write and integrate them!

Needs the creation of an organizational repo -- should be eligible for educational rates though.

Pinging @mkoo on this issue to give @n8upham some guidance.

1. Lets change "ASM Species Account Database" to "ASM Mammal Diversity Database"

2. in the "Search" can we make it a box? Its actually confusing (a bit) about where to click to start typing, whether on that line, or else below it with the blue bar where it says "Search for a common or scientific name above to begin, eg, "Brown Bear" or "Ursus arctos"" — it would be great to just move that blue bar up, with the identical text, and make that the "Search" entry form— Does that make sense?

3. Add the twitter bar on the right hand side, about 1/4 or 1/5 of the browser window width, similar to the WoRMs site: http://www.marinespecies.org/ ( see #32 )

4. Can we add a "News" listing under the search field to update folks about new releases of the taxonomy, popular press, etc.? I can write a blog entry for this when we go live

5. Creative ideas about a landing page image / beautification, etc? We want folks to be excited about mammals when they land here

Thanks man, --nate

• If it exists on IUCN but not on DB, fetch citation from IUCN
• If it exists on the DB, should feedback and block save until taxon changed

Marsupalia -> Marsupialia
Dasyuromorpha -> Dasyuromorphia

Errors from my database, thanks

species and subspecies are swapped

This should result in an edit dialog opening for this species for an admin

Via @n8upham @27:

Also, is adding a Twitter bar a difficult thing to do? I'm modeling this idea after the WoRMS database: http://www.marinespecies.org/

Remove it!

https://mammaldiversity.org/species-account.php?genus=abrawayaomys&species=ruschii

For the main text on the front page, can we use "ASM Mammal Diversity Database"?

And then to correspond, the site title (in the tab header on Firefox) to the same thing?

Thanks man
--nate

Doesn't open calphotos, and then opens a bazillion copies from overbinding.

Put at top of Taxon Entry as 'citations' to highlight it more.

Data citation entry should be multiline rather than single line.

"I was able to break the search by searching using the advanced options alone (nothing in the standard search box), all my queries returned the entire database. It might be better to label the advanced options as "filters" to narrow down the search results? Or perhaps just refuse to search if the standard search line is blank? I'm not sure which would be an easier fix. "

"On the statistics page, species diversity is plotted as a bar graph (appropriate), but generic diversity is plotted as a filled curve (not ideal). Let’s set a good example of appropriate use of graphs and use bar graphs for both categories."

Maybe side-by-side bar graphs, just slightly to the left or right for genera?

Thanks man (that was the last one!)

"When searching for something that doesn’t exist, a small badge pops up very briefly saying “no results”. It’s easy to miss this though. I’d rather have some stable text that stays put stating this."

"I agree with Jake about the "No Results" needing to be larger and more prominent. I didn't see it for some time while clicking search repeatedly. Also, it appears to be a dynamic, where it returns the fields that had no results...While trying to test the search limits, I was able to have it flash a very large no results box with every field mentioned. It flashed way too fast to read the whole text (I had to screenshot it to read)."

Meta issue to make sure this doesn't get lost in the lead-up to the ASM meeting.

How much work is involved in making the main search field == a query to all fields in the database? Would there be a cost of longer search times?

Also, when I search "Rodentia" under "Clade" the advanced search still returns no results. I think we want Clade to indicate Higher Taxon in general

Genus Authority does work (e.g., "Thomas" returns 8 results), but species authority returns no results for the same search...

Thanks, --n

Via @n8upham

Featured mammal = one of these 4 species with free Mammalian Species accounts: https://academic.oup.com/mspecies/pages/speciesaccounts

• The goal here is to
  1. showcase this ASM-based journal, and
  2. make an argument to the Board that we should be serving the content of these Mammalian Species articles for free on the MDD website. This would both populate our per-species pages and provide an outlet to these articles that often linger in obscurity, but contain much valuable information
• Check out that Felis margarita!

My initial response and thoughts:

I will need to ponder the featured mammal entry -- need to figure out a way to both accomplish the goal above and to keep search functions central and accessible.

My best off-the-cuff idea is an auto-opening dialog on first visit / featured taxon change, with some other button or iconography to expose it again manually (so it shows up immediately when it's new to you, but when you're going to the site to do a "routine" search you're not interrupted by content you've already seen before).

There may be a better solution, just I haven't thought of it yet.

Later response:

Yes I like the idea of a featured mammal tab that is popped out the first time, but not on subsequent visits. But maybe on the pop-out tab there can still be a small (thumbnail) version of the MIL image for that featured species? I want to have some mammal images on the front page, so people know there are here to learn about furry things!

Blocked on #20

• Orders capitalized
• Y-axis is great on log scale, but can you translate it to real numbers = 1,2,5,10,20,50,100, etc?
• Genera
  • capitalized
  • italics
• Display of a text-based table that shows the totals being visualized
• Ability to sort by descending taxon order? (not critically important if is difficult to implement that, folks can just download and analyze themselves)

E.g., I do a search on Primates and then only want to download the primates subet of the master taxonomy file— I can imagine users would like this.

"This box looks more like a search box than the actual search box. My first instinct was to not read the text in this box, but to just click and try to type. That doesn’t work. I suggest making this text look less like a search box. "

They're ignoring the extension and name set in the attribute.

See: https://bugs.chromium.org/p/chromium/issues/detail?id=735080

Needs to

• walk distinct genera
• Find oldest citation among unformatted (all) and formatted genera
• Apply oldest as genus citation for all of them
• Format and apply species citation

blocking #50

Connor found this one:
https://mammaldiversity.org/species-account.php?genus=utahraptor&species=ostrommaysorum

I'm working on arranging the final list now... more soon
--n

Note: Stretch goal for milestone! May not accomplish!

Could use the IUCN countries-by-taxon ( http://apiv3.iucnredlist.org/api/v3/docs#species-occurrence-name )

eg:

{"name":"Loxodonta africana","count":40,"result":[{"code":"AO","country":"Angola","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"BF","country":"Burkina Faso","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"BI","country":"Burundi","presence":"Extinct Post-1500","origin":"Native","distribution_code":"Regionally Extinct"},{"code":"BJ","country":"Benin","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"BW","country":"Botswana","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"CD","country":"Congo, The Democratic Republic of the","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"CF","country":"Central African Republic","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"CG","country":"Congo","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"CI","country":"Côte d'Ivoire","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"CM","country":"Cameroon","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"ER","country":"Eritrea","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"ET","country":"Ethiopia","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"GA","country":"Gabon","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"GH","country":"Ghana","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"GM","country":"Gambia","presence":"Extinct Post-1500","origin":"Native","distribution_code":"Regionally Extinct"},{"code":"GN","country":"Guinea","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"GQ","country":"Equatorial Guinea","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"GW","country":"Guinea-Bissau","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"KE","country":"Kenya","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"LR","country":"Liberia","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"ML","country":"Mali","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"MR","country":"Mauritania","presence":"Extinct Post-1500","origin":"Native","distribution_code":"Regionally Extinct"},{"code":"MW","country":"Malawi","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"MZ","country":"Mozambique","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"NA","country":"Namibia","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"NE","country":"Niger","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"NG","country":"Nigeria","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"RW","country":"Rwanda","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"SL","country":"Sierra Leone","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"SN","country":"Senegal","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"SO","country":"Somalia","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"SS","country":"South Sudan","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"SZ","country":"Swaziland","presence":"Extant","origin":"Reintroduced","distribution_code":"Reintroduced"},{"code":"TD","country":"Chad","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"TG","country":"Togo","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"TZ","country":"Tanzania, United Republic of","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"UG","country":"Uganda","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"ZA","country":"South Africa","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"ZM","country":"Zambia","presence":"Extant","origin":"Native","distribution_code":"Native"},{"code":"ZW","country":"Zimbabwe","presence":"Extant","origin":"Native","distribution_code":"Native"}]}

and do a color coded political map???

Reported by @n8upham

Whoops

We want this to be accessible from the front page on landing at the MDD. Ideally it would be based on the tree navigator at https://tree.opentreeoflife.org/opentree/argus/opentree9.1@ott93302

If this seems tricky, I can contact the PI on that project Karen Cranston

Let me know when you need an example tree file to base this navigator upon.

• Column citation for taxon entry citation
• Column genus_authority_citation
• Column species_authority_citation

These citations should be displayed on account pages:

• Genus authority
• Species authority
• Entry

How easy would it be to add a forum-type page where we could solicit feedback on the database and host a record of public discussion on taxonomic issues? This might be a "DISQUS" type thing in a centralized location (https://disqus.com/)

Also, is adding a Twitter bar a difficult thing to do? I'm modeling this idea after the WoRMS database: http://www.marinespecies.org/ See #32

Thanks, --n

@n8upham :

You mentioned in your email that the new list has 6301 new species. However, when I integrate and update the data, I get a new count of 6733.

It took a while to find the discrepancy, but I finally did.

For example, let's look at the genus Eospalax.

MariaDB [mammal2_asm_sadb]> select genus, species, internal_id from mammal_diversity_database where genus like 'eospalax' order by species;
+----------+-------------+-------------+
| genus    | species     | internal_id |
+----------+-------------+-------------+
| eospalax | baileyi     |   100000481 |
| eospalax | cansus      |   100000482 |
| eospalax | fontanierii |       14118 |
| eospalax | rothschildi |       14121 |
| eospalax | rufescens   |   100000483 |
| eospalax | smithii     |       14122 |
+----------+-------------+-------------+
6 rows in set (0.12 sec)

However, the base dataset you gave has this to say on the subject:

split from frontanierii

for sp = baileyi, cansus, and rufescens. They are tagged as splitFromExisting, but also have no entry under IfTransfer_oldSciName (implying the old taxon is still valid, and it's just been differentiated).

However, the dataset doesn't actually have fontanierii in it as a standalone taxon, making this ambiguous as to if it's been deprecated.

The size of this split from existing set seems to fully encompass the difference in counts.

For now, I'll operate under the assumption that both taxa are valid while I'm completing the data insertion/merge, but this ambiguity needs to be resolved!

Via @n8upham

Add a page called “Taxonomy” to the toolbar header— this page will contain sub-links and descriptions about the following:

• List of new species (since MSW3) and their citations for “evidence" and “name”, including links to the article where we have that info
• List of genus name transfers (since MSW3) and the citation for the change
• Summary table comparing counts of species, genera, and families in MSW3 versus our MDD list

It works on the main page, but from the summary or info pages it gives error that "cannot retrieve random entry" — all this is awesome though man!

See #51 (comment)

I want to eventually change this generation to a random entry from the ten longest, newest entries with an image rather than statically filled.

This will be nice for visitors to get a random glimpse of "more populated" pages
Thanks
--n

Provide an API endpoint to do structured and limited queries against the DB

May not even need regex for final deprecated since it's a controlled input...

Model this after the IUCN listing where they have a “Synonyms” field in their CSV output that includes data as e.g., "Abrothrix hershkovitzi|Abrothrix markhami|Akodon mansoensis |Akodon olivaceus |Akodon xanthorhinus”

So that is all recent name combinations as separated by pipes.

We can form that synonym pipes column using the 200k+ row listing that I sent you yesterday. Do you want me to work on parsing that, or are you already on it?