FL-Islandora IR Documentation

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Contents

Introduction

This page is the best place to check for up-to-date documentation on in development work on Islandora.

Note that as FLVC continues to do our own development the documentation may be out-of-date, and may refer to older code. If instructions seem to be incorrect, please email FLVC so that the instructions can be clarified or updated.

Info about ir-test

  • Here's the login url: https://ir-test.digital.flvc.org/user
    • The repository functionality is also set up on test sites for the following institutions: FAU, UCF, FGCU, and FSU.
  • The namespace on the ir-test site is "ir". So, all your Collection PIDs should start with "ir:". If you click "Ingest" to make a Collection, and don't see a collection, try again with the "ir:" namespace PID.
  • The following people have accounts on the ir-test site: Parker Fruehan, Devin Soper, Roxann Mouratidis, Jane Strudwick, Melissa VandeBurgt, Joanne Parandjuk, Lee Dotson, Bryan Brown, Favenzio Calvo, Chealsye Bowley. If anyone else needs a login, all of you are site admins, so you can make them a login. Feel free to add anyone else who needs an account.

Linking Departments, Scholars, and Publications

Diagram of Entity relationships:

IRentityRelationships.jpg

How to link an Organization Entity (department) to an Organization Entity (parent department)

Instructions:

1. FLVC creates a top level department "root department" for your organization. The Islandora system will identify this as the "root" of the "tree" for making the tree display which appears under the "Repository" link along the top of screens. You can see which department this is by going to your Islandora site, then clicking the "Repository" tab along the top. The very top level of your tree is the top level department specified by FLVC. (On ir-test, the root department is "Top Level Entity: Holds University/College Organizations".) You can click to it and edit the name, but if you delete it, then you must contact FLVC to make a new one.

2. Create an Organization Entity for the parent department.

2a. Link your parent department to the "root department" for your site: On your parent department, click the "Manage" tab, then click to "Datastreams", then click to "edit" MADS. Fill in the "Parent School/Faculty" with the Department Name of the root department. (On ir-test, the root department is "Top Level Entity: Holds University/College Organizations".)

2b. Fill in the parent department's Department Name with a unique name: Browse to the department you'd like to edit, then click the "Manage" tab, then click to "Datastreams", then click to "edit" MADS. Fill in the "Department Name" (stores in the MADS as <authority><name type="corporate"><namePart>). This will be shown to the user, so use actual department names as identifiers. Remember what string you entered in for "Department Name", because you will use this string to do the linking later.

3. Now create a child department and link it: Browse to the child department you'd like to edit, then click the "Manage" tab, then click to "Datastreams", then click to "edit" MADS. Fill in the "Parent School/Faculty" with the Department Name of the parent department. This has to be an exact same name - exact same letters and spaces in the same order.

4. The order matters when you edit parent and child departments. If you need to change the parent department's name later, you need to first change the "Department Name" in the parent department Organization Entity, then later edit the child department and add that new name in as the "Parent School/Faculty".

Note: This linking is done by a string match in the metadata.

How to link a Person Entity to an Organization Entity (department)

Instructions:

1. Create an Organization Entity for the department you'd like to represent.

2. Fill in the "Department Name" (stores in the MADS as <authority><name type="corporate"><namePart>). This will be shown to the user on each faculty member's profile, so use actual department names as identifiers. Remember what string you entered in for "Department Name", because you will use this string to do the linking later.

3. Now link the Person to the Organization. Go to the Person Entity you'd like to link, click the "Manage" tab, then click to "Datastreams", then click "edit MADS".

4. When editing the Person Entity's MADS, in the blank labeled "Department", start typing the name of the Department. When it autofills, use your mouse to click on the correct value to complete the value you would like to use. The department name is stored as a string in the Person entity's MADS in MADS field <affiliation><organization>, and displays on the person's profile under the heading for "Department(s)" and under "Other Scholars in..."

5. If you need to change the department name later, you need to first change the name in the department Organization Entity, then later edit the name in the MADS for every Person Entity linked to that department.

Note: The order you complete steps in matters. You must edit the Person Entity last, in order for Solr indexing to include information about the department in displays of the person.

Note: This link is done by a string match in the metadata.

How to link a publication to a Person Entity

Instructions:

1. Make sure the Person Entity has a unique identifier: Edit the Person Entity's MADS <identifier> field: Click to the Person Entity you are working wtih, then click to the "Manage" tab, then click to "Datastreams", then click to "edit MADS". In the form, edit the field labeled "Identifier".

2. Enter this identifier into the MODS for the content object: Edit the content object's MODS <name><nameIdentifier> field: Click to the content object you would like to link, then click to the "Manage" tab, then click to "Datastreams", then click to "edit MODS". Use the "Full MODS" form to edit the MODS. Under the "Names" area of that form look for "ORCID" and "Local NameIdentifier".

  • You would use the ORCID (MODS <name><nameIdentifier type="ORCID">), if you deployed ORCID on your campus.
  • You would use some other scheme (MODS <name><nameIdentifier type="local">), for example official campus email address, if you have not deployed ORCID on your campus.
  • (You can switch from "local" to "ORCID" easily one profile at a time. To do so, you would add the ORCID into the MODS for each publication, then after the metadata was all prepped, you would edit the Person Entity with the Scholar MADS Form and change the Identifier from your local one to an ORCID.)


Note: The link is done by a string match in the metadata.

Note: MADS <identifier> in the Person Entity links to MODS <name><nameIdentifier> in the content object.

How to link a publication to an Organization Entity (department)

1. Create the Organization Entity (department) for the department you'd like to represent.

  • Here's info on filling out the form fields for the Organization Entity (department).
    • Fill in the "Department Name" (stores in the MADS as <authority><name type="corporate"><namePart>). This will be shown to the user on each faculty member's profile, so use actual department names as identifiers. Remember what string you entered in for "Department Name", because you will use this string to do the linking later.

2. Link the publication to the Organization Entity using the MODS field for <name><affliation>Organization Entity's name goes here</affliation></name> .

  • Here's info on filling out the form fields for the publication:
    • Use the Full MODS Form.
    • In the "Names" area:
      • Under "Affliation", enter the name for the Organization Entity.

Superseded as of Sept. 2017 You cannot directly link a publication to an Organization Entity (department). Instead, you have to create an intermediate Person Entity, link that Person Entity (dummy representation of a department) to the Organization Entity (department), then link the publication to the Person Entity (dummy representation of a department).

1. Create the Organization Entity (department) for the department you'd like to represent.

  • Here's info on filling out the form fields for the Organization Entity (department).
    • Fill in the "Department Name" (stores in the MADS as <authority><name type="corporate"><namePart>). This will be shown to the user on each faculty member's profile, so use actual department names as identifiers. Remember what string you entered in for "Department Name", because you will use this string to do the linking later.

2. Create the Person Entity (dummy representation of a department).

  • Here's info on filling out form fields for the Person Entity:
    • For the "Given Name", enter "Other Publications of". For the "Family Name", enter the department name. For the "Display Name", enter "Other Publications of [the department's name goes here]". (None of these fields are used for linking, but this will show up to the public. This labeling convention should help to avoid confusion.)
    • Now link the Person to the Organization. In the Person Entity's "Affliation" "Department" form field, enter the Organization Entity's (department's) name. This will be used to link the Person to the Organization.
    • Under "Affliation" "Position", use the drop down menu to select "Other".
    • Fill in the Person Entity's identifier. In the "Identifier" form field, type in a unique identifier (unique among all Person Entities).

3. Link the publication to the Person Entity (dummy representation of a department). Make sure the Person Entity has a unique identifier (the "Identifier" form field). Enter this identifier into the MODS for the content object.

  • Here's info on filling out the form fields for the publication:
    • Use the Full MODS Form.
    • In the "Names" area:
      • Use the drop down menu to select "Type" equals "corporate". Under "Name Part", enter the full text department name (this will not be used by the software for linking, but may show up to the public). Under "Local NameIdentifier", enter the unique identifier for the Person Entity (dummy representation of a department).

Batch Importing Person Entities

It is possible to batch import scholar Person Entities. This is done by taking an Excel spreadsheet of metadata about the Person Entities, and saving as csv. The import can include information about what department each Person Entity is associated with, so you can build out your departments first, then batch import people into them. Currently, someone at FLVC has to do the batch load.

Here's how to do the batch load:

  • Download this spreadsheet add information on your faculty: https://fliirt.wiki.flvc.org/wiki/images/FLIIRT/d/dd/FLVCtemplateBatchImportPersonEntities.xlsx
    • For notes on what each field means, print this tear sheet and refer to it: https://fliirt.wiki.flvc.org/wiki/images/FLIIRT/a/ae/FLVC-BatchImportPersonEntities-DocumentationOfFields-Jan2017.xlsx
    • In particular, the DEPARTMENT field is used to link the Person Entity to the department Organization Entity. You should first create the department Organization Entity, then fill out the spreadsheet.
    • In particular, the IDENTIFIER column (and identifier type="u1" field) is used to link publications (ie. any content object in Islandora) to the Person Entity. You should pick an identifier scheme to use to assign unique identifiers to faculty. FLVC recommends using either email address or ORCID. This identifier will be visible to anyone looking at a faculty member's profile.
      • You can also include a local identifier (LOCAL_IDENTIFIER column) and an Orcid identifier (ORCID_IDENTIFIER column) in your faculty information. As of summer 2017, this will not be used by the software to link publications to people, but it may be helpful later to have the information stored in the MADS record.
    • All persons in a single spreadsheet will be loaded inside the same collection. If you want to store your Person objects in separate collections, then provide separate spreadsheets.
    • Repeating fields: If you want to repeat a field, then fill out that spreadsheet cell to have all the values in one cell separated by a tilde ~ . For example, to repeat a department, include all this in one cell: Department of Art~Department of Nursing~Department of Math
  • Contact help@flvc.org to have the spreadsheet checked and loaded. Put "Islandora" in the subject line, and in the email provide a link to the collection you'd like to have the Person objects loaded to.
  • FLVC will load it to your Islandora test site first, then we'll both review it, then load it to your Islandora production site.

New Embargo Functionality: Islandora Scholar Embargo

  • Note: FLVC has not yet looked at how to configure this. There are setting FLVC can get to, which librarians can't and those include allowing Islandora Scholar Embargo to be used with such and such a content model, and that kind of thing. You can get to Islandora Scholar Embargo on your test site, but assume that it's not fully configured. If you look at it, and want it to work differently, definitely make the ask.
  • Note: Since Islandora Scholar Embargo does not yet have a cannonical configuration, this page has background info rather than instructions.
  • Islandora Scholar Embargos.
    • Embargo by date range; not IP.
    • Can embargo at the datastream level.
  • Different from IP Embargo, which has already been on all Florida Islandora sites for years.
IslandoraScholarEmbargoVsIPembargo.png

Importing and Exporting citation metadata

Importing Metadata from Crossref DOIs, PMID, RIS, etc.

When you create a new content object (of any kind; Citation, Thesis, PDF, Large Image, etc.), Islandora Scholar allows you to prepopulate the MODS form with metadata imported from:

  • PMID (Pubmed)
  • DOI
  • An RIS file
  • An Endnote XML export

This works similar to importing with MARCXML.

Note: At this time, for production installs, this will not automatically be part of the roll out. This is because, similar to the MARCXML upload, the option to import metadata from DOI, MID, etc. will show up on upload across the site. So, for the majority of objects, it's an extra step to click through. On request, FLVC can enable it for one content model at a time (ie. DOI import can be enabled for Citation and PDF items on your site.

Batch DOI Import

Batch import by DOI has to be turned on for your site in order for it to work. If it’s turned on, then when you go to a Collection, then to the “Manage” tab, then to the “Collection” tab, then to “Batch Import Objects”, there will be another option besides “zip loader” and that option will be “DOI Importer”. Batch import by DOI will only work for the Citation content model, but the option will show up for other content models – don’t use DOI Importer for batch loading anything other than Citation or strange things will be created and might cause trouble. If you see that option to batch import using “DOI Importer”, then you can use a load file with DOIs each separated by a single space.

While starting out, try importing small batches, and check each batch carefully. Report any problems or any DOIs which won’t import, so that FLVC can keep track of these.

There is no way to import a PDF along with the batch load by DOI. Instead the batch load by DOI will create metadata only objects, then you would have to manually add the PDF later after load.

Exporting Citation Lists

One aspect of the software which is not enabled on FLVC sites is the ability to make a list of items and then export a list of citations as PDF, XML, or test. This will also allow export of list of publications by a faculty member.

By default, the software formats all cites to publications as if it is a scholarly article. So, some manual clean up is needed.

As of Fall 2017, there wasn't a decision to not enable this on the Islandora sites. Instead, it hasn't gotten much interest. If you are interested in it feel free to ask.

Statistics and Altmetrics

View and Download counts for content models

This is functionality which has now gone out to all Islandora sites, not just FLIIRT. Islandora collects some statistics through the software.

Altmetrics

The Citation content model on test and production sites is set up to show an altmetrics display. The PDF content model on test sites only is set up to show an altmetrics display. (The display in PDF objects is ready for approval by ISG, and will likely be rolled out to production sites in Fall 2017.)

Here's an example: http://diginole.lib.fsu.edu/islandora/object/fsu%3A368803 . In the "Full Description" tab, the colored band from almetric.com's free-of-charge API will show up under the download and view counts for the item. (FSU's site has social media icons, which is a custom display change just for the FSU site. These social media icons are not part of the altmetrics display, so you shouldn't see them on your site, unless social media icons is addressed by the ISG at some point in the future.)

The altmetrics display pulls from <identifier type="doi"> (or <identifier type="DOI"> ). This is in keeping with Library of Congress's user guide on MODS identifiers. See https://www.loc.gov/standards/mods/userguide/identifier.html .

If the object has MODS with a DOI in the <identifier type="doi"> field and that DOI is formatted like 10.1038/srep16860 ( software won't recognize it when it's formatted like a URL), then Islandora will hit altmetric.com's free-of-charge API. If altmetric.com shows no use, then the colored band won't show up. If altmetric.com shows some use, then the colored band will show up.

Duraspace's Islandora Scholar and Entities Documentation

Documentation from the Duraspace community describes a standard install of Islandora. This documentation may be of interest is the Islandora developer/admin documentation:

General Launch Plan: Launching an IR

  • Step 1: FLVC sets your test site up with FLIIRT software, and sets up the top level department (Organization Entity).
  • Step 2: Build out a department tree on your test site.
  • Step 3: Provide FLVC with a spreadsheet of faculty information for batch loading to your test site. FLVC will load this. Then you do quality control and email FLVC with any revisions (faculty can't be moved over from test to production, so when you email the revisions, FLVC will edit the load file so it can be ready to go for loading on production later).
  • Step 4: Work with linking publications to scholars on your test site. This will get you familiar with how the linking works.
  • Step 5: Work with FLVC to develop an institutional repository splash page similar to UPEI's http://www.islandscholar.ca or FSU's https://fsu.digital.flvc.org/repository . (This step is optional or can be done at a later date.)
  • Step 6: Begin to prepared metadata on your production site. You can begin to add the MODS <nameIdentifier> field to publications. Keep general notes on what collections you have touched up. Later, after you create the faculty on your production site, you will have metadata in place and then will request reindexing of the publications. Reindexing will get the faculty members (Person Entities) into the Solr indexing for each object and the software will link them up. The reason you might want the metadata in place early is that then you can do a fast launch and get all the links up in a day or two once reindexing is complete.
  • Step 7: FLVC sets your production site up with FLIIRT software, and sets up the top level department (Organization Entity).
  • Step 8: Manually copy over each department (Organization Entity) from test to production. When you do this, start out with the higher up parent/grandparent departments first, then work down to children then grandchildren. The reason for working in this order is that Solr indexing will look to the parent department in the MADS form, so you want that parent department to exist when you save the MADS record.
  • Step 9: After departments are fully moved over, request FLVC to batch load faculty to your production site. (You finalize departments (Organization Entities) first, because then as the faculty (Person Entities) are created, the Person Entities's will index the departments in Solr.) For this step, do quality control. Use the .csv import files, sort in Excel to get a count of faculty in each department, then click to the department in Islandora and ensure that the number of faculty showing up in each department is the same in Islandora as in the .csv load. Ultimately, what you are checking for is that all the letters and characters are perfect that are used for linking the faculty to departments.
  • Step 10: Request reindexing of publications on your production site. This will get the Solr of the publications to link up to the faculty and departments.
  • Step 11: Request FLVC to move over to production any splash pages that you worked with FLVC to create on test.
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