Scaling Science

Overview

We are leveraging methods from machine learning, artificial intelligence, databases, and graph theory to improve our ability to compute on scientific knowledge—and thus more intelligently plan, collaborate, and allocate resources to science. The end goal is the creation of a decentralized, community-focused scientific knowledge dissemination platform.

Data

For now, we are working with the publication metadata released by the Open Academic Graph project. This is a joining of the Microsoft Academic Graph and AMiner database.

In the future, we will move to active scraping and integration of ArXiv, BioRxiv, The PMC Open Access Subset, and other data sources. Of course, the end goal will be a platform that scientists submit work and results to directly, similar to Github.

Version control

Git. Please submit issues for new features and bugs, create branches when working on issues, and submit pull requests for merging back into master so everyone is synchronized.

Project management

We are using Github Projects to coordinate the work and issues in the different branches of this project.

Quick start

Run ./start_docker.sh to read/set some environmental variables and build and launch neo4j and jupyter notebook containers. Console will print a token-based authentication link to paste into your browser to connect to both the jupyter session and the neo4j broser portal. The Neo4j database is password protected via the credentials in the NEO4J_AUTH environmental variable set in docker-compose.yml.

Database Schema

Nodes

:Author

Relationships
(:Author)-[:AUTHORED]->(:Quanta)
(:Author)-[:COAUTHOR]-(:Author)
(:Author)-[:AFFILIATED_WITH]->(:Organization)
(:Author)-[:METRICS_IN]->(:Year)

property	type	index	unique	description
temporary	INTEGER
start_year	INTEGER			year the author's first paper was published
idMag	STRING
cleanName	STRING	TRUE
citations	INTEGER
name	STRING
hIndex	INTEGER
id	STRING	TRUE	TRUE
position	STRING			deprecated - part of :AUTHORED relt
normalizedName	STRING
lastAffiliation	STRING
numPublications	INTEGER
idAminer	STRING

:Quanta

Relationships
(:Author)-[:AUTHORED]->(:Quanta)
(:Quanta)-[:METRICS_IN]->(:Year)
(:Quanta)-[:PUBLISHED_IN]->(:Year)
(:Quanta)-[:CITES]->(:Quanta)
(:Quanta)-[:PUBLISHED_IN]->(:Venue)

property	type	index	unique	description
temporary	FLOAT
issue	STRING
year	INTEGER
docType	STRING
idv1	STRING	TRUE
language	STRING
abstract	STRING
title	STRING
idMag	STRING
volume	STRING
cleanName	STRING	TRUE
citations	INTEGER
publisher	STRING
id	STRING	TRUE	TRUE
idAminer	STRING
doi	STRING

:Venue

(:Venue)-[:METRICS_IN]-(:Year)
(:Quanta)-[:PUBLISHED_IN]->(:Venue)

property	type	index	unique	description
cleanName	STRING	TRUE
journalId	STRING
name	STRING
id	STRING	TRUE	TRUE
normalizedName	STRING
idMag	STRING
matchingId	STRING	TRUE
idAminer	STRING

:Year

(:Quanta)-[:PUBLISHED_IN]->(:Year)
(:Quanta)-[:METRICS_IN]->(:Year)
(:Author)-[:METRICS_IN]->(:Year)
(:Venue)-[:METRICS_IN]-(:Year)

property	type	index	unique	description
value	INTEGER	FALSE	FALSE

Relationships

(:Author)-[:AUTHORED]->(:Quanta)

(:Author)-[:COAUTHOR]-(:Author)

(:Author)-[:AFFILIATED_WITH]->(:Organization)

(:Author)-[:METRICS_IN]->(:Year)

property	type	description
authorAge	INTEGER	Years since first paper published
citations	INTEGER
citationsPerPaper	FLOAT
citationsPerPaperDelta	FLOAT	Change in mean cites per paper over last two years
hIndex	INTEGER
hIndexDelta	INTEGER	Change in h-index over the last two years
maxCitations	INTEGER	Max citations on a single paper author has received
pageRank	FLOAT	PageRank in coauthor graph
rankCitationsPerPaper	FLOAT	Rank of author (between 0 and 1) among all other authors in terms of mean citations per year
recentCoauthors	INTEGER	Total number of coauthors in last two years
totalCitations	INTEGER
totalCitationsDelta	INTEGER	Two year change in total citations
totalPapers	INTEGER
totalPapersDelta	INTEGER
totalVenues	INTEGER	Total number of venues author published in
venueCitationsPerPaperDeltaMax	FLOAT
venueCitationsPerPaperDeltaMean	FLOAT	Two year change in mean citations per paper of venues author has published in
venueCitationsPerPaperDeltaMin	FLOAT
venueCitationsPerPaperMax	FLOAT
venueCitationsPerPaperMean	FLOAT	Mean citations per paper of venues author has published in
venueCitationsPerPaperMin	FLOAT
venueHIndexDeltaMax	INTEGER
venueHIndexDeltaMean	FLOAT	Mean of 2-year h-index change for venues author has published in
venueHIndexDeltaMin	INTEGER
venueHIndexMax	INTEGER
venueHIndexMean	FLOAT	Mean of H-indices of venues author has published in
venueHIndexMin	INTEGER
venueMaxCitationsMax	INTEGER
venueMaxCitationsMean	FLOAT	Mean of maximum number of citations any paper published in a venue has received for each venue the author has published in
venueMaxCitationsMin	INTEGER
venueRankCitationsPerPaperMin	FLOAT
venueRankCitationsPerPaperMean	FLOAT	Ranks of venues (between 0-1) in which the author has published determined by mean number of citations per paper
venueRankCitationsPerPaperMax	FLOAT
venueTotalPapersDeltaMax	INTEGER
venueTotalPapersDeltaMean	FLOAT	Two year change in mean of the total number of papers published in venues author has published in
venueTotalPapersDeltaMin	INTEGER
venueTotalPapersMax	INTEGER
venueTotalPapersMean	FLOAT	Mean of the total number of papers published in venues author has published in
venueTotalPapersMin	INTEGER
weightedPageRank	FLOAT	In coauthor network

(:Quanta)-[:METRICS_IN]->(:Year)

(:Quanta)-[:PUBLISHED_IN]->(:Year)

(:Quanta)-[:CITES]->(:Quanta)

(:Quanta)-[:PUBLISHED_IN]->(:Venue)

(:Venue)-[:METRICS_IN]-(:Year)