open data hk: open science meets open data. a primer from scott edmunds
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Scott Edmunds
@SCEdmunds
@GigaScience
meets
Open science primer
Can this be considered open data?
http://biology.clc.uc.edu/fankhauser/labs/genetics/dna_isolation/thymus_dna.htm
Does this qualify as open source?
http://2011.igem.org/Team:UC_Davis
What is Open (Science) Data?
• Something very very very geeky
• Free & open access to data about the world around us
o Searchable, findable
o Machine-readable, app-makeable, Excel-usable
o Without restrictions/limitations
• This (examples)
About me:
• Scott Edmunds
• Molecular biology, sci editing & comms
• Scientific journal & (big) data publishing
• Reproducibility & open science
Journal, data-platform and database for
large-scale biological datawww.gigasciencejournal.com
About me:
• Formerly Beijing Genomics Institute
• Founded in 1999 (1% of HGP)
• China’s 1st citizen managed not-for-profit research institute funded by commercial sequencing-as-a-service (BGI Tech)
• Now largest genomic organization in the world
• HQ in Shenzhen, most data production in BGI HK (Tai Po)
About my employer:
Standing on the shoulders of giants
Open Data 1665?
Scholarly articles are merely advertisement of scholarship . The
actual scholarly artefacts, i.e. the data and computational
methods, which support the scholarship, remain largely inaccessible --- Jon B. Buckheit and David L. Donoho, WaveLaband reproducible research, 1995
Science Data Volumes
Exabytes Petabytes100’s of Petabytes
Sequencing
Mass Spec
Astrophysics HE Physics Biology
Imaging
Square Kilometer Array
Large Hadron Collider
Esoteric formats, poorly structured,
Tabular, often spreadsheet based
Issues open data community well used to (data cleaning, scraping, etc.,)
The long tail of scientific data…
?
Open Data in Physics1961 CERN pre-prints shelf
http://cerncourier.com/cws/article/cern/28654http://arxiv.org/
1991-date arXiv
Open Data in Biology
1934: newsletter era 1987: online era1980: database era 2010’s: “bioinformatics bingo” era
BGI HK Chamber O’Illumina’sThe LHC of Biology?
20PB of storage
Open Data in Chemistry
Closed Data in Chemistry
V
Genomics: open-data success story?
Sharing/reproducibility helped by stability of:
1. Platforms
1. Repositories
2. Standards
1st Gen 2nd Gen
:
Genomics Data Sharing Policies…
1. Automatic release of sequence assemblies within 24 hours.2. Immediate publication of finished annotated sequences.3. Aim to make the entire sequence freely available in the public domain for
both research and development in order to maximise benefits to society.
Bermuda Accords 1996/1997/1998:
1. Sequence traces from whole genome shotgun projects are to be deposited in a trace archive within one week of production.
2. Whole genome assemblies are to be deposited in a public nucleotide sequence database as soon as possible after the assembled sequence has met a set of quality evaluation criteria.
Fort Lauderdale Agreement, 2003:
The goal was to reaffirm and refine, where needed, the policies related to the early release of genomic data, and to extend, if possible, similar data release policies to other types of large biological datasets – whether from proteomics, biobanking or metabolite research.
Toronto International data release workshop, 2009:
0
100
200
300
400
500
600
700rice wheat
Rice v Wheat: consequences of publically available genome data.
Sharing aids fields…
Digitizing the world
Can we make everything open data?
NO
NO
The (non-) human centipede: first sequence
SOURCE
USER
NARRATIVE DATA
PUBLISHER
EXTERNAL
DATABASESARRAYEXPRESS
Morphbank
DATA PRODUCTION
CURATION/
INTEGRATION
• Genomics
• Barcoding
• Imaging
• microCT
• Video
(SOCIAL)
MEDIA
NO
What is open science? 5 flavours:
Benedikt Fecher and Sascha Friesike: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2272036
Democratic:
Biggest Challenge: Closed Access
WWW.RIGHTTORESEARCH.ORG
Biggest Challenge: Closed Access
Handful of closed access STM publishers control market
Force libraries to buy “bundles”
Revenue >$9B
Average cost /article >$5000 USD
Publishers retain copyright
Prevent data mining of content
Withold information from 99.9% who need it!
Biggest Challenge: Closed Access
Publishing: better than a gold mine
See: http://alexholcombe.wordpress.com/2013/01/09/scholarly-publishers-and-their-high-profits/
Increasing strain on library budgets
-50%
0%
50%
100%
150%
200%
250%
300%
350%
400%
1986 1988 1990 1992 1994 1996 1998 2000 2002 2004
Perc
enta
ge C
hange
Year
MIT library purchases v inflation 1986-2006
Consumer Price Index % + Serial Expenditures % + # Serials Purchased % +
# Books Purchased % + Book Expenditures % +
Journal expenditure
Inflation
Too expensive for Harvard…
The good news: the fightback has started…
http://thecostofknowledge.com/
The Solution: Open Access
“By “open access” to [peer-reviewed research literature], we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.”
Budapest Open Access Initiative:
• Maximizes reuse and access• Gives authors control over the integrity of their work and the right
to be properly acknowledged and cited.• “Real” OA asks for no restrictions/limitations = CC-BY
Hong Kong: off the map
https://www.openaccessbutton.org/
Push the button!
Hong Kong: still some work to go with OA
…Singapore beats us
Pragmatic:
Infrastructure:
Pragmatic/Infrastructure:
Wiki science:
• 10,000 distinct gene pages.• 1.42 million words and 78MB data. • 50 million views & 15,000 edits per year.
Crowdsourcing, wisdom of the masses
GeneWiki
GitHub science:
A hypothetical Git workflow for a scientific collaboration involving 3 authors. Karthik Ram: http://www.scfbm.org/content/8/1/7
http://en.wikipedia.org/wiki/Portal:Gene_Wiki
Open Lab Notebooks
To maximize its utility to the research community and aid those fighting the current epidemic, genomic data is released here into the public domain under a CC0 license. Until the publication of research papers on the assembly and whole-genome analysis of this isolate we would ask you to cite this dataset as:
Li, D; Xi, F; Zhao, M; Liang, Y; Chen, W; Cao, S; Xu, R; Wang, G; Wang, J; Zhang, Z; Li, Y; Cui, Y; Chang, C; Cui, C; Luo, Y; Qin, J; Li, S; Li, J; Peng, Y; Pu, F; Sun, Y; Chen,Y; Zong, Y; Ma, X; Yang, X; Cen, Z; Zhao, X; Chen, F; Yin, X; Song,Y ; Rohde, H; Li, Y; Wang, J; Wang, J and the Escherichia coli O104:H4 TY-2482 isolate genome sequencing consortium (2011) Genomic data from Escherichia coli O104:H4 isolate TY-2482. BGI Shenzhen. doi:10.5524/100001 http://dx.doi.org/10.5524/100001
Our crowdsourcing example:
To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to Genomic Data from the 2011 E. coli outbreak. This work is published from: China.
Downstream consequences:
“Last summer, biologist Andrew Kasarskis was eager to help decipher the genetic origin of the Escherichia coli strain that infected roughly 4,000 people in Germany between May and July. But he knew it that might take days for the lawyers at his company — Pacific Biosciences — to parse the agreements governing how his team could use data collected on the strain. Luckily, one team had released its data under a Creative Commons licence that allowed free use of the data, allowing Kasarskis and his colleagues to join the international research effort and publish their work without wasting time on legal wrangling.”
1. Citations (~180) 2. Therapeutics (primers, antimicrobials) 3. Platform Comparisons
4. Example for faster & more open science
1.3 The power of intelligently open dataThe benefits of intelligently open data were powerfully
illustrated by events following an outbreak of a severe gastro-
intestinal infection in Hamburg in Germany in May 2011. This
spread through several European countries and the
US, affecting about 4000 people and resulting in over 50
deaths. All tested positive for an unusual and little-known
Shiga-toxin–producing E. coli bacterium. The strain was initially
analysed by scientists at BGI-Shenzhen in China, working
together with those in Hamburg, and three days later a draft
genome was released under an open data licence. This
generated interest from bioinformaticians on four continents. 24
hours after the release of the genome it had been assembled.
Within a week two dozen reports had been filed on an open-
source site dedicated to the analysis of the strain. These
analyses provided crucial information about the strain’s
virulence and resistance genes – how it spreads and which
antibiotics are effective against it. They produced results in
time to help contain the outbreak. By July 2011, scientists
published papers based on this work. By opening up their early
sequencing results to international collaboration, researchers in
Hamburg produced results that were quickly tested by a wide
range of experts, used to produce new knowledge and
ultimately to control a public health emergency.
http://www.gov.hk/en/theme/psi/contest/contest_events.htm
Pragmatic/Infrastructure:
Open Innovation Challenges
http://www.scientificamerican.com/openinnovation/
Public:
Indie Science
Biohacker spaces
CoResearch labs
Crowdfunding
DIYbio
Open hardware
http://www.perlsteinlab.com/
Biggest crowdfunding successes
Utilizing students: iGEM
iGEM:
http://2011.igem.org/Team:UC_Davis
The “Peoples Parrot”Puerto Rican Parrot Genome Project (Amazona vittata )
Rarest parrot, national bird of Puerto Rico
Community funded from artworks, fashion shows, beer brands, crowdfunding…
Genome annotated by students in community college as part of bioinformatics education
Paper and Data published in GigaScience and GigaDB
Taras K Oleksyk, et al., (2012) A Locally Funded Puerto Rican Parrot (Amazona vittata) Genome Sequencing Project Increases Avian Data and Advances Young Researcher Education. GigaScience 2012, 1:14Steven J. O’Brien. (2012): Genome empowerment for the Puerto Rican parrot – Amazona vittata. GigaScience 2012, 1:13Oleksyk et al., (2012): Genomic data of the Puerto Rican Parrot (Amazona vittata) from a locally funded project. GigaScience. http://dx.doi.org/10.5524/100039
Public: Citizen Science
Galaxy Zoo:
Zoonoverse:
887,355 “Zooites” and counting
https://www.zooniverse.org/
Public: Citizen Science
1987-1997
http://sabap2.adu.org.za/
Public: Games with a Purpose
http://fold.it/http://www.sciencegamecenter.org/
https://apps.facebook.com/fraxinusgame/
OpenSciDev
http://openscidev.com/
1. What value framework is a prerequisite for open science?2. How can open science support visibility and communication of
science outside formal academic structures?3. How can open science create education?4. How can the economic and social value of open science be
measured?
• Writing working paper on these questions• Building networks across Africa, Asia, Latin America and the
Caribbean.• Setting up call for funding for OpenSciDev projects ($2-3M)
Questions asked:
Currently working on:
To summarize:
• Open data is more than just government data (although research data mostly is government funded too)
• Need for OA advocates & policies in Hong Kong (role for ODHK?)
• Much science community can still learn about open licensing
• Much wider open data community can learn on community engagement from Citizen Science, GWAP, etc.
• Asia (inc HK) behind US/EU on many of these activities, but can we learn lessons from success of iGEM and “Jamboreee” model? *…King+
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