Collecting the organizational scholarly record

@hvdsomp
VIVO Conference 2019, September 5 2019, Podgorica, Montenegro
Herbert Van de Sompel
DANS
@hvdsomp
https://orcid.org/0000-0002-0715-6126
Collecting the Organizational Scholarly Record

@hvdsomp
James Powell, Harihar Shankar, Marko Rodriguez, and Herbert Van de Sompel (2014) EgoSystem: Where are our
Alumni? code{4}lib journal, issue 24. https://journal.code4lib.org/articles/9519
2013 - EgoSystem

@hvdsomp
EgoSystem Team
• Los Alamos National Laboratory:
• James Powell
• Harihar Shankar
• Herbert Van de Sompel
• Aurellius:
• Marko Rodriguez

@hvdsomp
Motivation
• When postdocs leave LANL, the local information systems
maintain very little information about them
• But senior management is interested in engaging them after they
leave LANL as Ambassadors and Advocates
• They needs answers to questions like:
• Who is currently working where?
• Who is involved in what areas of research?
• Who might serve as advocates for the Lab?
• Who knows someone who knows someone we need to
connect with?

@hvdsomp
2012 - Initial Approach: Set Up a VIVO Instance
• 2700+ records were
ingested from LANL
Postdoc Office data to
create initial user profiles
• 8 postdoc alumni were
contacted to complete
their profile

@hvdsomp
• Up-to-date information at all times is essential to meet the need of
senior LANL management
• Some existing VIVO instances seemed to have been pre-
populated but then remained static after launch
• Would current and former postdocs be interested in
maintaining a professional profile on a VIVO instance
intended to help out LANL?
Doubts about the VIVO Instance

@hvdsomp
• Leverage public, network-level information pertaining to LANL
Alumni
• Find their network presences - social portals, scientific
portals, homepages, etc.
• Recurrently collect information from those presences: current
employer, social network neighborhood, geo location, etc.
• Create applications based on that information
• Rationale: People have incentives to keep network-layer
information up-to-date
• Goal: Devise a sustainable approach to gather and use up-
to-date information pertaining to LANL Alumni
2013 - New Approach: Leverage Network-Level Information

@hvdsomp

Available information elements for PostDocs:
• Z#
• Name
• Institutions:
o PhD University; LANL; Institution after
LANL
• Field of Study
• Discipline

Find network identities:
• Various queries based on information
elements in:
o Yahoo Boss API; MS Academic
Search API
• Search for candidate identities:
o LinkedIn; MS Academic; Twitter;
Homepage; Blogger; SlideShare;
WikiPedia
• Rank and select candidate identities
o Reward when: same identities from
various searches; content matches
information elements

@hvdsomp
LinkedIn Identity

@hvdsomp
Twitter Identity

Network-derived information:
• Identities:
o LinkedIn; MS Academic; Twitter;
Homepage; Blogger; SlideShare;
WikiPedia
• Additional information elements:
o Current institution; geo location;
updated discipline

@hvdsomp
0
200
400
600
800
1000
1200
1400
1600
1800
none one two three four five
Web Identities Discovered Per Postdoc

@hvdsomp
Resulting Identity Types per Postdoc
0
500
1000
1500
2000
2500
3000
3500
LANL MS Academic LinkedIn Twitter

@hvdsomp
• Random set of 100 postdocs
• MS Academic
o 86 correct
- 71 correctly discovered identities
- 15 correctly labeled as not having identity
o 14 incorrect
- 2 discovered identities did not match the postdoc
- 12 existing identities were not discovered
• Algorithms favored precision over recall
Evaluation of the Discovery Algorithm

@hvdsomp
Network-derived information:
• Network neighborhood:
o Social network ~ Twitter: followers,
followed
o Academic network ~ co-authors MS
Academic
o Affiliations ~ LinkedIn, homepage
• Artifacts: papers, slide decks
• Concepts

@hvdsomp
• Platonic vertices
o Persons
o Institutions
o Artifacts
o Concepts
• Affiliation vertices
o Different types
o Different time periods
• Graph extent, started with 3,005 postdocs:
o Vertices: 9,015,844
o Edges: 19,399,683
Property Graph Representation of Resulting Information

Property Graph Representation of Resulting Information

@hvdsomp
Graph Database for Storage/Retrieval/Analysis
Titan Distributed Graph Database
http://titan.thinkaurelius.com/

@hvdsomp
• Simple web query interface
• Shareable profile page for individuals
• Graph analytics (aggregate social networks, path analysis) and
graph visualization
• Who’s where (the LANL Director travels) search
• Capability to add non-LANL person to the graph
o To find closest path to the person via a LANL postdoc
EgoSystem Application

@hvdsomp
Success?
• At the end of the demo meeting, the director said (paraphrasing)
o “I didn’t know what I wanted when we first met but this looks
like what I want, what I need.”
• Project discontinued because of the inability to access LinkedIn
data in legitimate manner
• As a result of heuristic-based processes, the database, query
results are not necessarily correct/complete. This made
EgoSystem an approximating application.
• Fantastic 2 month (~ 6 MM) project that did not yield a production
system but in which we learned an awful lot

@hvdsomp
James Powell, Martin Klein, and Herbert Van de Sompel (2017) Autoload: a pipeline for expanding the holdings of
an Institutional Repository enabled by ResourceSync code{4}lib journal, issue 36.
https://journal.code4lib.org/articles/12427
2016 - Autoload

@hvdsomp
2018 – myresearch.institute
The Scholarly Orphans project
is funded by the Andrew W. Mellon Foundation

@hvdsomp
myresearch.institute Team
• Los Alamos National Laboratory:
• Lyudmila Balakireva
• Martin Klein
• James Powell
• Harihar Shankar
• Herbert Van de Sompel
• Old Dominion University:
• Sawood Alam
• Grant Atkins
• Shawn Jones
• Mat Kelly
• Michael L. Nelson

@hvdsomp
• Consideration
• Researchers are increasingly using a variety of web platforms for
collaboration and communication
• Why?
• Many of these platforms have desirable characteristics
• Versioning
• Time stamping
• Social embedding
• Their institutions do not provide platforms that have global reach
• Collaboration, cf. Github ~ productivity
• Communication, cf. SlideShare ~ visibility
Research and Research Communication on the Web

@hvdsomp
• Consideration
• Researchers are increasingly using a variety of web platforms for
collaboration and communication
• Web Platforms:
• Dedicated to scholarship:
• Commercial: e.g., FigShare, Publons
• Not for profit: e.g., OSF, Zenodo
• General purpose:
• Commercial: e.g., GitHub, SlideShare
• Not for profit: e.g., Wikipedia, Wikidata

@hvdsomp
Emma Schymanski
https://orcid.org/0000-0001-6868-8145
https://github.com/schymane
https://www.slideshare.net/EmmaSchymanski
https://figshare.com/authors/Emma_Schymanski/5087039
https://publons.com/author/1538491/emma-schymanski#profile
https://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/emma-schymanski/

@hvdsomp
Shawn Jones
https://orcid.org/0000-0002-4372-870X
http://www.shawnmjones.org/
https://github.com/shawnmjones
https://www.slideshare.net/shawnmjones
https://en.wikipedia.org/wiki/User:Shawnmjones
https://www.blogger.com/profile/17827543974149663194

@hvdsomp
• Consideration
• Researchers deposit artifacts in web platforms
• Status quo - The researchers’ institutions are in the dark
• Do not know about the existence of these artifact
• Do not have a copy of these artifacts

@hvdsomp
• Consideration
• Status quo – Uncertainty regarding long-term access
• Commercial: changing business model, no preservation commitment
• Not for profit: unpredictable funding stream

@hvdsomp
• Consideration
• Status quo - Not systematically archived
• No frameworks like LOCKSS/Portico exist for these artifacts
• Researchers only selectively deposit artifacts in portals that
provide archival guarantees; to obtain a cite-able DOI
• Can’t expect researchers to (also) upload all artifacts in IRs
• Web archives only incidentally archive these artifacts, cf.
anecdotal & Hiberlink project evidence
Martin Klein, Herbert Van de Sompel, et al. (2014) Scholarly context not found. In: PLOS ONE
https://doi.org/10.1371/journal.pone.0115253

@hvdsomp
Emma’s SlideShare Artifact: 0 Mementos
https://www.slideshare.net/EmmaSchymanski/dmcm2018-community-resources-connecting-chemistry-and-toxicity-knowledge
http://timetravel.mementoweb.org/

@hvdsomp
Shawn’s GitHub Artifact: 1 Memento
https://github.com/shawnmjones/mediawiki
https://web.archive.org/web/*/https://github.com/shawnmjones/mediawiki

@hvdsomp
Evidence from the Hiberlink Project
Web resources referenced in Elsevier corpus (1996-2012)
without representative Memento in public web archives

@hvdsomp
The Scholarly Orphans Project: How to Archive these Artifacts?
• Explores an institution-driven paradigm
• Academic institutions typically have a long shelf life
• A basic premise underlying e.g., LOCKSS, perma.cc
• An academic institution should be interested in capturing the
artifacts (intellectual property) its scholars deposit on the web
• Collecting and archiving such artifacts aligns with the
mission of academic libraries

@hvdsomp
An Institutional Perspective

@hvdsomp
The Scholarly Orphans Project: How to Archive these Artifacts?
• Explores a paradigm inspired by web archiving
• Scale of the problem
• Can’t expect researchers to upload all artifacts in an institutional
repository
• Bilateral agreements for archival purposes with most web
portals unlikely

@hvdsomp
A Web Archiving Perspective

@hvdsomp
myresearch.institute Prototype Pipeline

@hvdsomp
Tracking Artifacts

@hvdsomp
Tracking Artifacts - Description
• In order to track artifacts that were recently deposited by an
institutional researcher in a portal, one reasonably needs:
• The web identity of the researcher in the portal
• Algorithmic discovery, cf. EgoSystem
• Discovery via a registry, cf. ORCID paper
• Manual collection
• A portal API that supports:
• Access by web identity
• Access to contributions “since …” for the web identity
• Result of tracking:
• URI(s) of new artifact(s) discovered in the portal
Klein, M., and Van de Sompel, H. (2017) Discovering Scholarly Orphans Using ORCID. Proceedings of the 2017
ACM/IEEE Joint Conference on Digital Libraries https://arxiv.org/abs/1703.09343

@hvdsomp
Tracking Artifacts - Challenges
• Portal API access by web identity
• Broadly supported by general purpose portals
• Typically not supported by scholarly portals
• Some lack an API altogether
• Should add ORCID access to APIs
• OAI-PMH and ResourceSync need sets per web identity
• Professional versus personal contributions

@hvdsomp
Capturing Artifacts

@hvdsomp
Capturing Artifacts - Description
• The capture process takes as input the URI of a new artifact
discovered in a portal
• Its task is to create a representative institutional capture of the
artifact
• Result of capture:
• WARC file for new artifact in an institutional archive

@hvdsomp
Capturing Artifacts - Challenges
• Create a high-fidelity capture using an approach that scales for a
steady stream of new artifacts
• Handle dynamic content & interactive features of web pages
• Determine the web boundary of the artifact
• More than the input artifact URI
• The boundary is in the eye of the beholder
• We made a significant breakthrough with the Memento Tracer
framework
• Others (cf. webrecorder.io Autopilot, IA Brozzler) are working on
the same problem
Memento Tracer: http://tracer.mementoweb.org
Autopilot: https://blog.webrecorder.io/2019/08/14/autopilot
Brozzler: https://github.com/internetarchive/brozzler

@hvdsomp
Memento Tracer - Framework
http://tracer.mementoweb.org

@hvdsomp
Archiving Artifacts

@hvdsomp
Archiving Artifacts - Description
• The archiving process takes as input the URI of a WARC file
generated by the capture process
• Its task is to ingest the WARC file in a cross-institutional web archive
• This can be achieved using off-the-shelf web archiving software,
e.g., pywb, Open Wayback
• Result of archiving:
• Mementos pertaining to newly discovered artifact in a cross-
institutional, Memento-compliant web archive

@hvdsomp
Archiving Artifacts - Challenges
• Attempted to use ipwb, a pywb version that uses IPFS
• Cross-institutional distributed file system with redundancy
• Ran out of time to get it operationally stable
Sawood Alam, Mat Kelly, and Michael L. Nelson (2016) InterPlanetary Wayback: The Permanent Web Archive
https://doi.org/10.1145/2910896.2925467

@hvdsomp
myresearch.institute - Researchers
• Uniquely identified by ORCIDs
• Web identities in multiple portals
• Create various types of artifacts

@hvdsomp
myresearch.institute - Portals
• Tracking started August 27 2018
• Tracking artifacts created starting
August 1 2018

@hvdsomp
Scholarly Orphans – Pipeline
• 16,005 unique artifacts tracked, captured, and archived between
20180801 and 20190828
• 60MB event database
• 83GB of WARC files
• 3GB of web archive index

@hvdsomp
Showtime: myresearch.institute Portal
https://myresearchinstitute.org

@hvdsomp
Success?
• “Interesting project! I’m happy to participate.”
“One more thing, is it possible to get a copy of the URI-Rs that
you guys detected so that I can feed them into an archive of my
choice?...”
• Prototype pipeline developed over 8 months (24 MM)
• Metrics of the prototype demonstrate that researchers generate
a lot of artifacts (that their institutions are typically not aware of)
• Metrics of the prototype suggest it should be possible to run a
production pipeline at the scale of an academic institution
• But would they …?

@hvdsomp
Some Final Thoughts
• For a number of reasons, applications that leverage network-level
information at scale (e.g. EgoSystem, myresearch.institute,
Autoload) tend not to be perfect. But they are automatic.
• Do institutions reserve sufficient resources for innovation and
failure? The alternative seems to be outsourcing and loss of
expertise.
• Ideas/visions are rarely fully realized when working on them. But
many times, the work does improve on the status quo. So keep
dreaming and working!

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