Create a new taxon name+classification

This describes one method of creating a new name in Arctos, while bringing along classification data.

First, make sure the “new” name does actually exist….

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…and does not exist in Arctos….

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Then find the “donor” name, in this case http://arctos.database.museum/name/Otus%20flammeolus

Find the “donor” classification, and click “Clone Classification as new name.”

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Enter the new name and the intended classification source, click create.

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You will be redirected to the edit classification page – edit and rearrange things appropriately, carefully following the embedded instructions.

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Carefully check for any now-incorrect terms that may have come along with the clone process. Click save.

Check everything again. If it all looks good, click “Edit Non-Classification Data.”

Create relationships and common names as necessary. A relationship will ensure that users searching for Otus flammeolus specimens can find Psiloscops flammeolus specimens.

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Save everything, click “Return to taxon overview” (here¬†http://arctos.database.museum/name/Psiloscops%20flammeolus). Review everything again.

The name and classification is now usable.

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To improve discoverability, click the “Refresh/pull GlobalNames” link to import alternate classifications from GlobalNames. The page will refresh with any available GlobalNames data. (There are none for this taxon.)

Locality Update

THIS PAGE DOCUMENTS AN ARCTOS RELEASE SCHEDULED FOR JULY 9 2012.


Locality Documentation

This document supercedes all other locality documentation.

Major changes to the model (and, partially, their implications) are summarized here.

Specimens lose their (singular) pointer to place information; cataloged_item.collecting_event_id is no more.

Geography (geog_auth_rec) exists as a parent to locality, as before.

Geology (geology_attributes) exists as a child of locality, as before.

Table lat_long is gone. Coordinates are now a part of Locality data (and recorded verbatim in collecting_event). Note that nothing suggests coordinates are determined from locality data; in this model, coordinates can stand as the primary or only place information.

One implication of this change is that there is no longer a 1specimen–>1acceptedCoordiate relationship: Any specimen can have lots of (or no) coordinates which could be considered accepted for various purposes. The FLAT data objects (which are used for specimen search and results, among other things) deal with this (kinda…) by grabbing a random set of coordinates from a random “accepted place of collection” specimen_event. Better ideas for representing the actual complexity are as always welcome.

Reports that use lat_long will no longer work. Feel free to use the data from FLAT for reports and such, but do please be aware that our world is no longer necessarily so flat and that it is possible to link a specimen to multiple events of various types. (Handy for things that spend some time in captivity, biopsies, mark-recapture data, etc.) I’m happy to help resurrect your reports – just let me know what no longer works and how it should work under the new model.

Along the same lines, the specimen_event_type vocabulary could use some help. There are currently two options, representing accepted (or NULL) versus unaccepted coordinate determinations.

Unless someone yells vigorously and soon, this will deprecate catalog.cfm – I simply don’t think it’s possible to make people aware of the complexity of the data from that form under this model.

Table Locality is now

ColumnName NULLability DataType Explanation
LOCALITY_ID NOT NULL NUMBER primary key
GEOG_AUTH_REC_ID NOT NULL NUMBER foreign key to table geog_auth_rec
SPEC_LOCALITY NULL VARCHAR2(255) Locality descriptor
DEC_LAT NULL NUMBER(12,10) Decimal latitude; eventually to be calculated WGS84 decimal latitude
DEC_LONG NULL NUMBER(13,10) Decimal longitude; eventually to be calculated WGS84 decimal longitude
MINIMUM_ELEVATION NULL NUMBER minimum numeric elevation
MAXIMUM_ELEVATION NULL NUMBER maximum numeric elevation
ORIG_ELEV_UNITS NULL VARCHAR2(30) from ctorig_elev_units
MIN_DEPTH      
MAX_DEPTH      
DEPTH_UNITS      
MAX_ERROR_DISTANCE      
MAX_ERROR_UNITS      
DATUM      
LOCALITY_REMARKS      
GEOREFERENCE_SOURCE      
GEOREFERENCE_PROTOCOL      
LOCALITY_NAME     Assigned unique name for the locality; useful in grouping specimens and data entry.

New table specimen_event links specimens to places.

ColumnName NULLability DataType Explanation
SPECIMEN_EVENT_ID NOT NULL NUMBER primary key
COLLECTING_EVENT_ID NOT NULL NUMBER foreign key to collecting_event
COLLECTION_OBJECT_ID NOT NULL NUMBER foreign key to cataloged_item
ASSIGNED_BY_AGENT_ID NOT NULL NUMBER Person who made the specimen/event linkage
ASSIGNED_DATE NOT NULL DATE date on which the linkage was established
SPECIMEN_EVENT_REMARK      
SPECIMEN_EVENT_TYPE   NOT NULL ctspecimen_event_type
COLLECTING_METHOD NULL VARCHAR2(255)  
COLLECTING_SOURCE NULL VARCHAR2(60) ctcollecting_source
VERIFICATIONSTATUS NULL VARCHAR2(255) ctverification_status; “verified by %” values lock events and places.
HABITAT NULL VARCHAR2(255)  

There may be zero or many specimen_events of any type for any specimen.

All habitat information is centralized in specimen_event.

How to use DOI/PMID to create Arctos publications

As of November 2011, Arctos has undergone major surgery in how Publications are created.

First, some history:

“Formatted Publications” were dynamically created by concatenating publication information (such as title and page numbers) together with Agent Names. Along with requiring information that was not useful for locating specimens (“show me specimens published on page 32….”), this often required the creation of new agents and/or agent names. This was a lot of work for little or no return, and often improperly used anyway. A trigger used some very complex logic to pull all this together into a “proper” citation, and when that failed (e.g., due to nonstandard page numbering) you were just out of luck. We learned a lot from this structure, but it never felt quite right.

Now, the current situation by way of example. (I’m making up the details; only the publication is real. Apologies to the people whose personal details I am going to get entirely wrong.) Let’s say there’s been a loan of (very) old moth specimens to Maria E. McNamara and her graduate student Derek E. G. Briggs. This (theoretical) loan results in a (real) publication – Fossilized Biophotonic Nanostructures Reveal the Original Colors of 47-Million-Year-Old Moths. The publication includes additional authors who are not in Arctos, were not part of the loan, and who are not important to demonstrating the usefulness of our collections.

There is a DOI given in the publication. Copy that, open the “create publication” form in Arctos. Paste the DOI (10.1371/journal.pbio.1001200) excluding any prefix¬† (“doi:” and “http://dx.doi.org/” are common) into the appropriate box, and click “[ crossref ].”

The DOI lookup service was able to obtain metadata, and everything you see above is the result of that one click. If you click “create publication” at this point, you would create a usable publication to which Citations could be attached, and which could be a part of Projects.

Here, however, we wish to capture agent information for at least the two authors to whom we’ve made our earlier (fake) loan. During the crossref lookup, Arctos has first looked for agents who match the string provided by DOI, then for agents who MIGHT match the string provided by DOI. All names – not just preferred – are considered. A maximum of 5 “suggestions” are returned for each of the first 5 authors.

The first agent returned by the DOI service is Maria E. McNamara. There is no agent with the exact name “Maria E. McNamara” in Arctos, but there are 3 agents with last name “McNamara,” all suggested in the first line of the blue Agents grid. We happen to know that “Marie Englewood McNamara” is correct, so we click that entry to select her.

The second author, who we also care about because he was on the loan, is “Derek E. G. Briggs.” Derek is also a pre-existing Arctos agent, and that agent happens to have an exact-match agent string available. Arctos finds and suggests only this agent, and again one click is all that’s necessary to add him to the publication.

The third author, Patrick J. Orr, does not have an exact name match in Arctos, and does not have a last name match in Arctos, so the system has gone off looking for agents with any string matching “Orr.” In this case, the results are not useful and can simply be ignored. If Patrick J. were deemed important, he would need to be added and selected in the standard way. If there were 6 “Orr” agents, Patrick J. might still not show up in the suggest list, but could be found in the standard way of picking agents. Take-home message: The agent suggestions are just suggestions. Sometimes they’re useful, and sometimes they’re not. Make no assumptions from them.

If we select the two suggested agents and create the publication….

we can then locate it by any name of either of two the authors who we added

or anything from the “full citation”

including the authors that we did not explicitly include

but we can NOT find the publication by authors (as “Participants”) that we did not include

results in

We could have used PMID (PubMed ID) rather than DOI to roughly the same affect. Note that PMID and DOI are apparently independently created and do not return the same values (“Maria E. McNamara” vs. “Maria E McNamara,” etc.).

Formatting from either source is occasionally horrible, and you are encouraged to use the formatting tools provided (or your method of choice) to rid citations of things like ALL CAPS and missing or excessive punctuation.

Most of the time, using DOI or PMID will create better (as in fewer mistakes) publications with much less work than traditional means. The service is, however, not magic and you, the operator, are responsible for the results. Your collections may have additional guidelines as to what agents to include, or how to format publications.

What are Media?

Here we provide a few examples of Arctos Media. This is not meant to be a comprehensive list, but rather a sampling of current Media helpful in understanding the breadth of Arctos’ non-specimen content. Arctos Media and their relationships are dynamic things, and we never really know what all is in there!

The most basic Media are those showing specimens. These may be found by requiring Media with any other specimen search criteria.

This will return specimen records which have Media – in this case, diagnostic pictures of lemming teeth created for an undergraduate rodent key project. Similar searches will find images of dinosaur bones, beached whales, herbarium sheets, eggs and egg data slips, and steppe bison.

Non-specimen Media may be located from the Media Search interface. These include historic landscapes, habitat, wildlife and evidence of wildlife, people, teaching material, accession data, locality cards, undergraduate projects, taxonomic treatments, and necropsy reports.

Media include images and their accompanying high-resolution DNG originals, field audio recordings, PDFs, and video. Media may be arranged as multi-page documents, and these may include TAGs that point to people, places, or specimens.

Customizing Arctos headers with CSS

[ copied from http://arctosblog.blogspot.com/2010/06/customizing-arctos-headers-with-css.html ]

* IMPORTANT *

You will want to try this out in TEST before moving to production!

You must coordinate loading all images with the development team, or host them on your own site.

* IMPORTANT *

To customize the header for your collection, you may simply supply the required values under Manage Collections.

To customize beyond the defaults, you’ll need to create a CSS file, coordinate loading it with the developers, and select it under STYLESHEET on the Manage Collection form.

Example: Use a dark background image for the header, and change the header links to be white for contrast.

Create a transparent-background logo approximately 100px in height. Load to Arctos (you’ll need developer assistance), and select the image in HEADER_IMAGE. Set HEADER_COLOR to “white” or it will override your image with gray.
Create a background image of height=1px less than the logo you created in (1).
Create a CSS file. (// signifies a comment below. This is not valid CSS comment syntax!)
// header_color is the ID of Arctos header
#header_color {
// this is the background image
background:url(“/images/DMNSHeaderBg2.png”) repeat-x scroll 0 0 #1C3664;
}
// change the color for the large text
.headerInstitutionText, .headerCollectionText{
color:white;
}
// and the links at the top-right
#headerLinks, #headerLinks a {
color:white;
size:small;
}
// add hover behavior to differentiate the links from text
#headerLinks a:hover {
color:red;
}