11 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

Scientific Publishing in the Future

Mark B Gerstein

Yale

with

D GreenbaumM SeringhausR AuerbachK CheungP BourneS Fields

Slides at Lectures.GersteinLab.org (See Last Slide for References & More Info.)

22 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

The Situation: a Changing

Landscape between "Info. Resources" &Traditional Journals

• Explosion of Web Information Resources

• DBs & Journals- Ends of blurring spectrum

• Reading articles from "queries" & "Mining" journal text

• Reading DB entries • Biology as science of

heterogeneous facts- What's vehicle for

annotating each base of genome ?

2

(c

) M

ark

Ge

rste

in,

20

02

, Y

ale

, b

ioin

fo.m

bb

.ya

le.e

du

[Nat. Biotech. 21:979; Bioinformatics 15:429]

EMBLNAR DB Issue

33 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

An Aspect of the Situation: Hard to fit everything into conventional

journal articles or biological DBs

• Many other aspects of a "citatable paper" than just narrative text- for computational biology: code downloads, annotation sets- for expt. biology: reagents, apparatus, &c.... - associated lectures and easy-to-read summaries, videos

(scivee) • Readability of Narrative Decreasing

- Data embedded into papers, making text hard to read• Data aliquot for DBs

- DB handle huge homogenous datasets but what of isolated facts

[BMC Bioinformatics 8:17 ; PLoS Comp. Bio. 4: e1000037]

44 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

Potential Directions Forward:Between Extremes

• Stay with Traditional Paper- "3 author" narrative on a conceptual advance- "Hard currency" of scientific discovery & advancement

• Move to Blogs, Websites, &c.- Posts, freeware distributions, DB depositions &c- Reference "Marker Papers", just shells

• Hypothetical "1 Million Genomes" consortium "marker", associated with many pieces of software, datasets, &c which not fully explained in article

• Take Middle Way- Structured and multi-tiered scientific literature

more compatible with the digital world

55 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

Structured, Multi-tiered Digital Paper Proposal

• "Broadened," Multi-tiered papers- Narrative text +

easy-to-read lay version + structured, mach. readable vers.

- Extended Suppl. material, containing data & code

- associated lectures, videos

• "Structured" Tier- for automatic deposition into DBs

& textmining - Cross-referencing with a specific

part of the genome, proteome, &c- Written as annotation from start

• All tiers submitted in parallel- Refereed & edited normally

• Incentives- Capitalizes on peer review &

incentives to publish- Authors (not currators) in control

of process- But officiated by referees and

editors

• A Path Forward- Abstract, Tables, Figures,

Equations..... eventually all

[Cheung et al. MSB ('10, in press); FEBS Lett 582: 1170; Nature 447: 142]

66 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

Ex. Structured Abstract

• K.lactis (species)- KlSTE4 (gene)

• KlSte4p (protein)– CLONED

* Available at …– SEQUENCED

* Sequence ATGTACGCTATAGGC….– MUTANTS

* DELETION* FUNCTIONAL ASSAYS* Sterile in both MATa and MATα* No defect in vegetative growth* STRAIN INFORMATION* Available at….

– INTERACTIONS* TWO-HYBRID* KlGpa1p (10x stronger) = XXX* Control (no partner) = XXX* KlGpa1p* = XXX* KlGpa2p = XXX* ScGpa1p = XXX (S. cerevisiae)¯¯¯¯

- KlGPA1 (gene)• KlGpa1p (protein)

– INTERACTIONS* TWO-HYBRID* KlSte4 = XXX

• KlGpa1p* (protein)– INTERACTIONS

* TWO-HYBRID* KlSte4 = XXX

- KlGPA2 (gene)• KlGpa2p (protein)

– INTERACTIONS* TWO-HYBRID* KlSte4 = XXX

• S.cerevisiae (species)- SCGPA1 (gene)

• ScGpa1p (protein)– INTERACTIONS

* TWO-HYBRID* KlSte4 = XXX

[BM

C B

ioin

form

atic

s 8

:17

]

77 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

Structured Digital Table

• Canonical Table Types

• Using standardized journal tables as small "stubbs" for larger datasets

[Cheung et al., MSB ('10) in press]

88 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

99 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

Default Theme

• Default Outline Level 1- Level 2

1010 -

Lec

ture

s.G

erst

ein

Lab

.org

(c)

'09

More Information on this Talk

SUBJECT: Textmining

DESCRIPTION:

PLOS Workshop at ISMB 2010: Where & How to Get Publishhere & How to Get Published, 2010.07.13, 10:45-12:45; [I:ISMB10] (5' total)

NOTES:This PPT should work on mac & PC.