The document discusses how Wikipedia has become a massive collaborative platform for scientific communication and summarization of the biomedical literature, with key points being:
1) The biomedical literature is growing rapidly but individual scientists cannot read it all, while Wikipedia provides summarization of concepts through "Gene Wiki" pages.
2) "Gene Wiki" pages have received over 4 million views per month and have over 1.4 million words of content from thousands of editors.
3) The Gene Wiki allows for a timely, reliable, and current review article to exist for nearly every gene.
Crowdsourcing to structure biological knowledge (USC/ISI)Andrew Su
Talk given at USC's Information Sciences Institute (http://www.isi.edu). The AV recording is pretty horrible, but for anyone interested: http://webcasterms1.isi.edu/mediasite/SilverlightPlayer/Default.aspx?peid=89751f8537c44f2fa241db99c793cd231d
A listing of databases that can be used to find information on environmental health topics. Note: Access to many of these resources is restricted - contact your local library to see if you have access.
Crowdsourcing to structure biological knowledge (USC/ISI)Andrew Su
Talk given at USC's Information Sciences Institute (http://www.isi.edu). The AV recording is pretty horrible, but for anyone interested: http://webcasterms1.isi.edu/mediasite/SilverlightPlayer/Default.aspx?peid=89751f8537c44f2fa241db99c793cd231d
A listing of databases that can be used to find information on environmental health topics. Note: Access to many of these resources is restricted - contact your local library to see if you have access.
J. Ingram, D. Poulcharidis - Adv. Topics of Chem. Bio. - Dr. Webb - Prof. S. ...JDIngram
A presentation on the O'Connor group, given as part of the Advanced Topics of Chemical Biology module. Yet to be awarded a mark, I presented from slide 6 onwards.
Chromosomes, Crops and Superdomestication - Pat Heslop-Harrison MalaysiaPat (JS) Heslop-Harrison
PUBLIC SEMINAR At Agro-Biotechnology Institute, ABI Serdang
Prof J. S. “Pat” Heslop-Harrison,
University of Leicester
Academic Icon, University of Malaya
Chromosomes, Crops and Superdomestication
Crop improvement is reliant on the exploitation of new biodiversity and new combinations of diversity. I will discuss our work on genome structure and evolution, involving processes including polyploidy, introgression, recombination and repetitive DNA changes. Identification and measurement of diversity and relationships assists in use of new gene combinations or new crops, through synthesizing new hybrid species, by chromosome engineering or by transgenic strategies. We are studying crops including wheat, Brassica and banana, using genome sequencing, repetitive sequence comparison, and cytogenetics. Plants, pathogens and farmers have been involved in a three-way fight since the start of agriculture, and the concept of superdomestication involves systematic identification of needs from crops, only then followed by finding appropriate characters and bringing them together in new varieties. Crops will continue to deliver the products needed for food, fibre, fuel and fibre in an increasingly sustainable and safe manner.
Astrocytes are neuroprotective glial cells that protect and nourish neurons of the central nervous systems. Rauwolfia vomitoria is a common medicinal plant used for the treatment of various diseases such as insanity, insomnia, hypertension, malaria etc. The comparative examination of reactive astrocytes in the cerebral cortex of adult albino wistar rats following the administration of crude ethanolic root bark and leaf extract of Rauwolfia vomitoria was studied using 25 mature Wistar rats of both sexes. The animals were divided into 5 groups, labeled A, B, C, D, and E. Group A was the control, while groups B, C, D, and E were the experimental. Oral doses of 200 mg/kg and 300 mg/kg body weight of the root bark extract were administered to groups B and C animals, while groups D and E animals received 200 mg/kg and 300 mg/kg body weight of the leaf extract respectively for seven days. On the 8th day, the rats were sacrificed; their brains were surgically extracted, and routinely processed for neurohistological study of Astrocytes using Hortegas lithium carbonate method for reactive astrocytes. Results showed hyperplasia of reactive astrocytes in the root bark groups, while there was hypertrophy of reactive astrocytes in the leaf extract groups when compared to the controls. Thus, the plant may have some adverse effects on neurons within the cerebral cortex.
This talk was given as a guest lecture in the undergraduate "Comparative Animal Physiology" course at the University of Texas at Austin. The talk has three parts: 1) a very brief personal introduciton about me and my thesis research, 2) an overview of some brain regions and genes that regulate social behaviors in birds, frogs, fish, reptiles, and mammals, 3) a discussion of a study looking at neuromolecular differences between closely related with with different mating systems.
J. Ingram, D. Poulcharidis - Adv. Topics of Chem. Bio. - Dr. Webb - Prof. S. ...JDIngram
A presentation on the O'Connor group, given as part of the Advanced Topics of Chemical Biology module. Yet to be awarded a mark, I presented from slide 6 onwards.
Chromosomes, Crops and Superdomestication - Pat Heslop-Harrison MalaysiaPat (JS) Heslop-Harrison
PUBLIC SEMINAR At Agro-Biotechnology Institute, ABI Serdang
Prof J. S. “Pat” Heslop-Harrison,
University of Leicester
Academic Icon, University of Malaya
Chromosomes, Crops and Superdomestication
Crop improvement is reliant on the exploitation of new biodiversity and new combinations of diversity. I will discuss our work on genome structure and evolution, involving processes including polyploidy, introgression, recombination and repetitive DNA changes. Identification and measurement of diversity and relationships assists in use of new gene combinations or new crops, through synthesizing new hybrid species, by chromosome engineering or by transgenic strategies. We are studying crops including wheat, Brassica and banana, using genome sequencing, repetitive sequence comparison, and cytogenetics. Plants, pathogens and farmers have been involved in a three-way fight since the start of agriculture, and the concept of superdomestication involves systematic identification of needs from crops, only then followed by finding appropriate characters and bringing them together in new varieties. Crops will continue to deliver the products needed for food, fibre, fuel and fibre in an increasingly sustainable and safe manner.
Astrocytes are neuroprotective glial cells that protect and nourish neurons of the central nervous systems. Rauwolfia vomitoria is a common medicinal plant used for the treatment of various diseases such as insanity, insomnia, hypertension, malaria etc. The comparative examination of reactive astrocytes in the cerebral cortex of adult albino wistar rats following the administration of crude ethanolic root bark and leaf extract of Rauwolfia vomitoria was studied using 25 mature Wistar rats of both sexes. The animals were divided into 5 groups, labeled A, B, C, D, and E. Group A was the control, while groups B, C, D, and E were the experimental. Oral doses of 200 mg/kg and 300 mg/kg body weight of the root bark extract were administered to groups B and C animals, while groups D and E animals received 200 mg/kg and 300 mg/kg body weight of the leaf extract respectively for seven days. On the 8th day, the rats were sacrificed; their brains were surgically extracted, and routinely processed for neurohistological study of Astrocytes using Hortegas lithium carbonate method for reactive astrocytes. Results showed hyperplasia of reactive astrocytes in the root bark groups, while there was hypertrophy of reactive astrocytes in the leaf extract groups when compared to the controls. Thus, the plant may have some adverse effects on neurons within the cerebral cortex.
This talk was given as a guest lecture in the undergraduate "Comparative Animal Physiology" course at the University of Texas at Austin. The talk has three parts: 1) a very brief personal introduciton about me and my thesis research, 2) an overview of some brain regions and genes that regulate social behaviors in birds, frogs, fish, reptiles, and mammals, 3) a discussion of a study looking at neuromolecular differences between closely related with with different mating systems.
Citizen Science and Rare Disease ResearchAndrew Su
Talk given at "Personalized Health in the Digital Age" September 22, 2016 at Campus Biotech in Geneva, Switzerland https://www.personalizedhealth2016.ch/
Centralized Model Organism Database (Biocuration 2014 poster)Andrew Su
A Centralized Model Organism Database (CMOD) for the Long Tail of Genomes
Presented at Biocuration 2014 in Toronto http://biocuration2014.events.oicr.on.ca/
See related slides at http://www.slideshare.net/andrewsu/20140116-gmod-short
A Centralized Model Organism Database (CMOD) for the Long Tail of Sequenced G...Andrew Su
Keynote talk given at GMOD 2014
Video of talk at: https://www.youtube.com/watch?v=RVijs5ry05E
Video of QA at: https://www.youtube.com/watch?v=dGHXo-iNsyU
Blog post: http://sulab.org/2013/06/creating-a-centralized-model-organism-database-cmod/
Crowdsourcing Biology: The Gene Wiki, BioGPS and GeneGames.org
Wikipedia as an engine for scientific communication and collaboration at massive scale
1. Wikipedia as an engine for
scientific communication and
collaboration at massive scale
Andrew Su, Ph.D.
@andrewsu
asu@scripps.edu
http://sulab.org OK
ScienceWriters2012 OK
October 27, 2012
2. 2
The biomedical literature is growing rapidly
Number of PubMed-indexed articles
1,000,000
800,000
600,000
400,000
200,000
0
1979 1984 1989 1994 1999 2004 2009
3. 3
The biomedical literature is growing rapidly
Average of articlesof humantypical scientist
Number capacity read by scientist
20
10
0
1979 1984 1989 1994 1999 2004 2009
7. 7
10k gene “stubs” within Wikipedia ≈ “Gene Wiki”
Protein structure
Gene
summary
Symbols and
identifiers
Gene Ontology
annotations
Protein
interactions
Tissue expression
Linked pattern
references
Links to structured
databases
Huss, PLoS Biol, 2008
8. 8
Gene Wiki has a critical mass of readers
Rank 1001-1010: Specialists Rank 101-110: Scientists
CSDA Tau protein
CNTNAP2 Interleukin 10
IGSF8 APC
Adenosine A3 receptor C-Met
RYR1 Factor V
ETV6 Interleukin 8
Small heterodimer partner CD44
5-HT1D receptor Histamine H1 receptor
TRPC6 Kappa Opioid receptor
Interleukin-6 receptor Dihydrofolate reductase
Rank 1-10: Laypeople
Total: 4.0 million views / month
Insulin
Titin
Human chorionic gonadotropin
Vasopressin
ANKH
CLOCK
Catalase
Erythropoietin
Glucagon
Parathyroid hormone
Huss, PLoS Biol, 2008; Huss, NAR, 2010; Good, NAR, 2011
9. 9
Gene Wiki has a critical mass of readers
Huss, PLoS Biol, 2008; Huss, NAR, 2010; Good, NAR, 2011
10. 10
Gene Wiki has a critical mass of editors
Editor count Editors
Edit count
Edits
Increase of ~10,000 words / month from >1,000 edits
Currently 1.42 million words
Approximately equal to 230 full-length articles
Huss, NAR, 2010; Good, NAR, 2011
11. 11
A review article for every gene is powerful
Reelin: 98 editors, 703 edits since July 2002
Hyperlinks to related concepts
Heparin: 358 editors, 654 edits since June 2003
AMPK: 109 editors, 203 edits since March 2004
RNAi: 394 editors, 994 edits since October 2002
References to the literature
12. 12
The Gene Wiki is timely and current
Manny Ramirez
suspended for doping
Catalase linked to
premature gray hair
Also, MGAT2 (obesity), ALDH2 (heart attack), SOX21 (hair
loss), SATB1 (breast cancer), TSLP (asthma), CCR5 (HIV), …
Huss, NAR, 2010
13. 13
The Gene Wiki is (reasonably) reliable
Per edit Average Probability
probability lifetime by time
Cumulative edits
Good edits 98.9% 115.4 d 99.968%
Vandalism 1.1% 3.4 d 0.032%
Date (0.63% for
WP overall)
Good, NAR, 2011
14. 14
Making the Gene Wiki more reliable
Novartis is a multinational 2 The company name is derived
pharmaceutical company from old Greek, and means
based in Basel, Switzerland "destroyer of birds".
that manufactures drugs such
as clozapine
(Clozaril), diclofenac
(Voltaren), …
2
Good, NAR, 2011 http://www.wikitrust.net/
15. 15
Making the Gene Wiki more reliable
Novartis is a multinational 2 The company name is derived
pharmaceutical company from old Greek, and means
based in Basel, Switzerland "destroyer of birds".
that manufactures drugs such
as clozapine
(Clozaril), diclofenac
(Voltaren), …
36211 total edits 36 total edits
* *
*
*
* *
*
* *
*
* *
* *
High-trust author Low-trust author
Good, NAR, 2011 http://www.wikitrust.net/
19. 19
Collaborators Group members
Doug Howe, ZFIN Ben Good Max Nanis
John Hogenesch, U Penn
Jon Huss, GNF
Salvatore Loguercio Chunlei Wu
Luca de Alfaro, UCSC Ian Macleod
Angel Pizzaro, U Penn
Faramarz Valafar, SDSU
Pierre Lindenbaum,
Fondation Jean Dausset
Michael Martone, Rush
Konrad Koehler, Karo Bio
Warren Kibbe, Simon Lim, Northwestern
http://slideshare.com/andrewsu
Many Wikipedia editors
WP:MCB Project
Contact
http://sulab.org
asu@scripps.edu
@andrewsu
+Andrew Su
Funding and Support
(BioGPS: GM83924, Gene Wiki: GM089820)
Editor's Notes
next gen sequencing identifies candidate genesAlso Microarray data, proteomics, GWAS, methylation, post-translational modifications, translocation detection, etc.What do these genes do?
Relying on the entire community of scientists to digest the biomedical literature: identification filtering extraction summarization
Relying on the entire community of scientists to digest the biomedical literature: identification filtering extraction summarization