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README.md

Build Status

Research Organization Registry (ROR) API

Between 2016 and 2018, a group of 17 organizations with a shared purpose invested their time and energy into an "Org ID" initiative, with the goal of defining requirements for an open, community-led organization identifier registry. Part of this investigation involved evaluating existing datasets that might provide seed data for a community-led system. To do this, we created a testing framework that would allow us to test two broad use-cases for using organization identifiers in the context of collecting affiliation data:

  • Supervised selection. Providing a UX that would allow researchers to easily and unambiguously select their affiliation. The ideal in this case is that a researcher should be able to type in a potentially ambiguous affiliation string, and the system would allow them to autocomplete the field with the correct and unambiguous affiliation name and identifier. Success in this scenario was if the correct affiliation was listed in the top five matches in the respective database.
  • Unsupervised matching. Providing a service that would allow a party to automatically bulk-match ambiguous affiliation strings against the respective databases. Success in this scenario was if the first match was the correct match. Note that, when testing this use case, we used a very naive matching system- not one that we'd expect to use in production. This means all the datasets probably scored lower than they would in a real implementation.

Repository contents

This repository contains sample code to explore matching of affiliation data from scientific papers against various databases of institutional identifiers.

The primary goal is to help assess how well the different databases can perform in matching against real-world affiliation data.

With this in mind the code is structured to make it relatively straight-forward to:

  • add a new dataset to the test suite
  • manage a set of simple search indexes using elastic search
  • prepare some affiliation data for testing
  • run a set of test affiliation data against the indexes
  • tinker with alternative elastic search queries (in so far as the indexes support them)

To a lesser extent the project may also have a role in surfacing general issues around matching of affiliations.

Table of Contents

Quick Start

The code is built against Ruby 2.4.0 and Java 1.8. You'll also need Bundler installed.

  • Checkout the project.
  • Run bundle install
  • In one terminal window, launch Elastic Search: rake server:start
  • Download and unpack the datasets and create the default indexes: rake setup:all
  • Convert the datasets into standard JSON format and load into Elastic Search: rake prepare:all (may take a while)
  • Run matching against the provided test data: rake report:match["config/crossref-sample.csv"]
  • Take a look at the CSV files in the data directory.

Run rake -T to get a list of the tasks.

There's support for converting individual files, reindexing, etc.

It's also worth installing the Sense Chrome Extension to allow manually exploring the Elastic Search indexes.

Dataset Configuration

The scripts work off a dataset configuration file which can be found at config/datasets.json. The file declares which datasets are being used, along with their name, version and a download link:

{
  "grid": {
    "name": "grid.ac",
    "version": "2017-04-04",
    "download": "https://ndownloader.figshare.com/files/7988347",
    "script": "bin/convert-grid.rb"
  },
  "gleif": {
    "name": "GLEIF",
    "version": "2017-05-04",
    "download": "https://www.gleif.org/lei-files/20170504/GLEIF/20170504-GLEIF-concatenated-file.zip",
    "script": "bin/convert-gleif.rb"
  }
}

Running rake setup:download (which is called automatically from setup:all) downloads the datasets, and rake setup:unpack unpacks them. The unpacked datasets can be found in data/grid, data/gleif, etc.

The dataset ids used in that file are used to uniquely identify the dataset across the rest of the scripts and configuration.

Adding New Public Datasets

If you're working with datasets that can be downloaded from the public internet, then you'll need to:

  • Declare the dataset in the configuration file
  • Write a script to convert the dataset into the standard JSON format (see below), adding the name of the script in the script section of the dataset config
  • Ensure that any sample datasets you're using to test matches include a column name for the dataset (see below)

Your conversion script should generate its output into the data directory using the dataset id in the filename, e.g. data/org-id-grid.json". Seebin/convert-gridandbin/convert-gleif` for examples.

With that in place the scripts will automatically find and index the data, query the index when matching, etc.

Adding "Private" Datasets

If you're working with private and/or local data, then you'll need to:

  • Declare the dataset in the configuration file
  • Manually download or export the dataset so it can be processed
  • Write a script to convert the dataset into the standard JSON format (see below), adding the name of the script in the script section of the dataset config
  • Ensure that any sample datasets you're using to test matches include a column name for the dataset (see below)

Obviously if you're able to export the private dataset directly in the desired JSON format (see next section) then there's no need to add a conversion script.

For example, the PSI dataset uses a sample database export which is not included in this project. The export was loaded into a local MySQL instance, exported as CSV into the data/psi directory where it can be processed by the bin/convert-psi.rb script.

See [PSI.md] for further notes.

Intermediary JSON Format and Index Structure

For loading into ElasticSearch, all of the datasets should be normalised into a simple common JSON format. This currently looks like:

{
 "orgs": [
    {
     "id": "grid.1001.0",
     "name": "Australian National University",
     "country": {
       "country-code": "AU",
       "country-name": "Australia"
     },
     "types" : [
          "Education"
     ]
    }
 ]
}

This is liable to change.

At the moment only a single name is indexed for each institution, but a more robust approach would allow for additional names. This might include translations, alternative forms of the name, previous names, etc.

Both a country name and code are included to facilitate full-text searching where the affiliation name might include the name of the country, whilst also allowing more precise matching using the country code (ISO Alpha 2 codes).

At present the testing has assumed a single country (location) for each institution.

The institution types aren't used yet, but are captured for now to allow exploration of filtering based on type.

Creating affiliation data for testing

An input CSV file should have the following structure:

Source,Affiliation,Institution,Country,DOI,ORCID,gleif,grid,psi
CrossRef,U.S. Army Research Laboratory; Adelphi Maryland USA,U.S. Army Research Laboratory,US,10.1002/2014rs005601,,N/A,grid.420282.e,N/A

  • Source - identifier for source of the data (currently ignored)
  • Affiliation - full, original affiliation text
  • Institution - the affiliation without any location information
  • Country - the ISO Alpha 2 country code for the institition country (if known)
  • DOI - source DOI for the data (for provenance, currently ignored)
  • ORCID - ORCID for the author with this affiliation (for provenance, currently ignored)
  • gleif - GLEIF identifier for this institution
  • grid - GRID identifier for this institution
  • psi - PSI identifier for this institution
  • ... - additional columns for other configured datasets

The separate Institution and Country are used to test alternative approaches for automatically matching affiliations. Whereas the Affiliation column contains the original affiliation, the other columns extract our the institution name and country code.

Populating these columns and the known matches against the various datasets has been done manually.

The following sections have some notes on how the sample affiliation data was collected and manually matched against the datasets.

Collecting Sample Crossref Data

There's a script that will generate sample data in this structured by taking a random sample of around 50 affiliations directly from the CrossRef API.

Run it using rake prepare:collect_crossref_samples. It will create a file called data/crossref-sample.csv

The config/crossref-sample.csv file included in the distribution was originally generated using that script. But it has been manually edited to:

  • Remove any erroneous affiliations, e.g. "None" and "Japanese Journal of Comparative Economics"
  • Populate the Institution by stripping any address, city or country information from the Affiliation column
  • Populate the Country column using any country information from the Affiliation. Left empty if there was no country data included in the original affiliation
  • Populate the gleif column by manually searching the GLEIF website
  • Populate the grid column by manually searching the GRID website
  • Populate the psi column by manually searching the PSI extract (see [PSI.md])

Where necessary additional Google searches were done to help clarify that the correct institution had been identified.

Collecting Sample ORCID Data

ORCID don't have an easy way to collect a random sample. So the process I used was to:

  • Download the public data file
  • Extract a list of the JSON files included in the file to create a separate index
  • Select a large random sample of entries from that index and extract them from the tar file
  • Set $ORCID_DATA to location of where the JSON files are
  • run rake prepare:collect_orcid_samples to create data/orcid-sample.csv

E.g: assuming the downloaded public data file is in ~/data/orcid and this project is in ~/projects/org-id

cd ~/data/orcid
tar tf ORCID_public_data_file_2016.tar > orcids.lst
grep json  orcids.lst >orcid-json.lst
tar -xvf ORCID_public_data_file_2016.tar `shuf -n 250 orcid-json.lst`
cd ~/projects/org-id
export ORCID_DATA=~/data/orcid/json
rake prepare:collect_orcid_samples

This was largely to avoid unpacking the entire archive whilst still selecting a relatively random selection of ORICDS.

If you have the disk space, then you could just download and unpack the extract, set the environment variable and then run the script to extract all records with affiliations.

The config/orcid-sample.csv file was originally generated using that script. But the CSV file was then manually edited to:

  • Remove any erroneous affiliations, e.g. "Full Professor"
  • Populate the gleif column by manually searching the GLEIF website
  • Populate the grid column by manually searching the GRID website
  • Populate the psi column by manually searching the PSI extract (see [PSI.md])

The Affiliation, Institution and Country columns are automatically populated as the ORCID data is cleaner than what we get from the CrossRef API.

Where necessary additional Google searches were done to help clarify that the correct institution had been identified.

Matching

By taking actual affiliation that has been manually matched against the datasets being tested, we can test the accuracy of the automated matching routines against each of the datasets. We can then compare the datasets based on their ability to match real world affiliation data.

The matching code can be run as follows:

rake report:match["config/crossref-sample.csv"]

This runs a script that will process the specified CSV file and attempt to match each of the affiliations against every dataset. The CSV file should be in the format documented in Creating affiliation data for testing.

Three benchmark sample files are currently provided:

  • config/crossref-sample.csv -- 50 affiliations taken from CrossRef with known matches against gleif, grid, psi
  • config/orcid-sample.csv -- as above, but taken from ORCID profiles
  • config/crossref-sample.csv -- combination of the two files

In addition to this a couple of test files have been provided that have NOT been matched against the datasets, so do not have known results. They're provided to explore output of the matching on a larger sample size:

  • config/crossref-1000.csv -- 1000 affiliations taken from CrossRef. Contains duplicates
  • config/crossref-1000-cermine.csv -- above file, but Institution and Country columns have been populated using the CERMINE API

To generate similar files you can run:

rake prepare:crossref_samples[1000] #generates data/crossref-sample.csv with 1000 rows
rake prepare:enrich_cermine[data/crossref-sample] #generates data/crossref-sample-cermine.csv

Matching reports

The output of the matching script is written to a collection of CSV files in the data directory.

The file naming is based on the input file.

Using the config/crossref-sample.csv as input, the script will generate the following files:

  • data/crossref-sample-report-basic-grid.csv
  • data/crossref-sample-report-basic-gleif.csv
  • data/crossref-sample-report-basic-psi.csv
  • data/crossref-sample-report-institution-grid.csv
  • data/crossref-sample-report-institution-gleif.csv
  • data/crossref-sample-report-institution-psi.csv
  • data/crossref-sample-report-summary.csv

There is one file for every dataset generated using two different matching routines (see below). Basically the input CSV file is enriched to include additional columns describing the best-match for the given dataset and matching routine.

The new columns are:

  • match-id -- the identifier of the best match
  • match-score -- the Elastic Search score for that match
  • match-name -- the institution name (for comparison)
  • match-success -- whether the match-id is same as the expected match in the source data

The summary file contains an overview of the number of potential and actual matches for each combination of datasets and matching routine. Potential matches are those where the institution is known to be present in the dataset.

The matching routines

Only two basic searches so far:

  • basic: A multifield search of the full Affiliation text against the _all field in the datasets index. This will match both the insitution name as well as the country code and name
  • institution: A combination query that searches for the Institution text in the name field in the index, whilst filtering against the country code (if available)

More routines could be added by revising the bin/report-matching script.

Comparing Country Coverage

When the datasets have been loaded into Elastic Search, the index can be used to generate a report on the country coverage for each of the datasets.

rake report:geo_coverage

This generates data/report-geo-coverage.csv that contains the total number of institutions by country and dataset.

Useful to just get a sense of the size and make up of the datasets.

Preconfigured Test Datasets

Notes on the tests datasets currently included in the configuration.

GLEIF

  • Global Legal Identifier
  • CC0 licensed dataset of legal identifiers for organisations
  • Contains around 500k records
  • As can be seen in config/crossref-sample.csv it has very few entries for universities and similar research organisations

Currently when indexing this dataset we use the location of the headquarters, rather than the legal address. The legal address isn't necessarily the primary work location for the organisation.

Institution names are often in the source language, e.g. as registered in the country of origin. This doesn't necessarily match what we find in affiliations which are often in English.

GRID

At the moment we're ignoring multiple locations, etc when indexing this dataset.

PSI

This is a private dataset, and was remmoved from this testing framewwork after these experiments were conducted. References to the PSI dataset still exist in the example UIs, but obviously they will not work without the data.

Wikidata

  • Wikidata
  • CC0 licensed dataset, collaboratively created by volunteers
  • 262,497 identifiers in the Company-EducationalOrg-Institution subset

For this project only a subset of the wikidata organisation identifiers have been used. This is due to the difficulty in retrieving a complete dataset via the Wikidata API. For now the subset consists of all Companies, Educational Organisations and Institutions. Even so this subset consists of a significant number of organisations.

Using a subset does mean that some types of organisations are not included, e.g. medical or government offices. However the breadth of organisations in Wikidata is very large: it includes bands, clubs, societies, teams, etc.

In the benchmark dataset, 13 organisations are known to be in the full wikidata dataset, but are not included in the Company-EducationalOrg-Institution subset. This includes 8 from the CrossRef affiliations and 5 from ORCID. Examples include "U.S. Army Research Laboratory" and the "Royal Darwin Hospital".

This needs to be taken into account when considering the wikidata scores.

A more robust approach would be to take a complete data export from wikidata, load it into a local RDF database to allow the full dataset to be extracted without hitting query time-outs. However this dataset was large enough for an initial test.

Open ISNI

  • Open ISNI
  • CC0 licensed dataset, published by Ringgold to share ISNI dientifiers
  • Contains around 400k records

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