punkish: Open Access, Open Source, Open Data

name: intro
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# Open Access, Open Source, Open Data
## the three pillars of open science

• April 2015

Puneet Kishor (Plazi)

Released under a [CC0 Public Domain Dedication](https://creativecommons.org/publicdomain/zero/1.0/).

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## The Three Pillars of Open Science

.three-left-column[
  ## Open Access
  
  Peer-reviewed and published journal articles and conference proceedings as well as non-peer-reviewed output such as popular articles, books, slideshows and videos
  
]

.three-mid-column[
  ## Open Source
  
  Software used in the analysis and visualization of data
  
]

.three-right-column[
  ## Open Data
  
  Data are the fuel of science
  
]

---

## [The FreeGIS Project](http://freegis.org)

> Provides software overview on Free Geographic Information Systems, and 
communication on developments, plans, infos on Free GIS Software and Free Geo-Data through a mailing list.

* Software (356)
* Geo-Data (25)
* Documents (19)
* Projects (10)

---

## [Directory of Open Access Journals](https://doaj.org)

> DOAJ is an online directory that indexes and provides access to high quality, open access, peer-reviewed journals.

* 10,441 Journals
* 6,261 searchable at Article level
* 136 Countries
* 1,879,128 Articles

---

## [Directory of Open Access Repositories](http://opendoar.org)

> OpenDOAR is an authoritative directory of academic open access repositories.

* 2600 repositories

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## Open Access…

[Public Library of Science aka PLOS](http://plos.org)

> PLOS (Public Library of Science) is a nonprofit publisher and advocacy organization founded to accelerate progress in science and medicine by leading a transformation in research communication.

[PeerJ](http://peerj.com)

> If we can set a goal to sequence the Human Genome for $99, 
then why shouldn't we demand the same goal for the publication of research?

[eLife](http://elifescience.org)

> Pain-free publishing for your best science.

---

## Open Access

[BioMed Central](http://biomedcentral.com)

> BioMed Central is an STM (Science, Technology and Medicine) publisher of 278 peer-reviewed open access journals.

[Ubiquity Press](http://ubiquitypress.com)

> Ubiquity Press is an open access publisher of peer-reviewed academic journals, books and data. We operate a highly cost-efficient model that makes quality open access publishing affordable for everyone.

[Pensoft](http://pensoft.net)

> Pensoft is an independent academic publishing company, well known among biodiversity scientists worldwide for technologically cutting-edge open access journals.

---

## Open Software (Frontend)

[QGIS](http://qgis.org)

> A Free and Open Source Geographic Information System. Create, edit, visualise, analyse and publish geospatial information. For Windows, Mac, Linux, BSD and Android.

[gvSIG](http://www.gvsig.com/en/products/gvsig-desktop)

> A powerful, user-friendly, interoperable GIS, designed to be an easily extensible solution, allowing thus continually improving the software application and developing tailor made solutions.

[GRASS](http://grass.itc.it/)

> GRASS GIS has raster, topological vector, image processing, volume voxel management/visualization, 2D/3D vector engine with vector network analysis and graphics production functionality that operates on various platforms through shell and a graphical user interface.

---

## Open Software (Backend)

[MapServer](http://mapserver.org)

> An Open Source platform for publishing spatial data and interactive mapping applications to the web.

[GeoServer](http://geoserver.org)

> GeoServer is an open source server for sharing geospatial data.

[Mapnik](http://mapnik.org)

> Mapnik is a Free Toolkit for developing mapping applications.

---

## Open Data…

[Global Change Master Directory](http://gcmd.nasa.gov)

> The GCMD holds more than 34,000 Earth science data set and service descriptions, which cover subject areas within the Earth and environmental sciences.

[GEOSS Portal](http://www.geoportal.org/web/guest/geo_home_stp)

> The GEOSS Portal is your main entry point to Earth Observation data from all over the world.

[OpenStreetMap](http://www.openstreetmap.org/)

> OpenStreetMap is a map of the world, created by people like you and free to use under an open license.

---

## Open Data…

[Shuttle Radar Topography Mission](http://www2.jpl.nasa.gov/srtm/)

> The Shuttle Radar Topography Mission collected topographic data in 2000 over nearly 80 percent of Earth's land surfaces, creating the first-ever near-global data set of land elevations.

[The National Map Viewer](http://viewer.nationalmap.gov/viewer/)

> Allows visualization and download of USGS's most current topographic base map data and products for free.

[National Water Information Service](http://waterdata.usgs.gov/nwis/rt)

> Water-resources data collected at approximately 1.5 million sites in all 50 States, the District of Columbia, Puerto Rico, the Virgin Islands, Guam, American Samoa and the Commonwealth of the Northern Mariana Islands.

---

## Open Data…

[Natural Earth](http://www.naturalearthdata.com/)

> Natural Earth is a public domain map dataset available at 1:10m, 1:50m, and 1:110 million scales. Featuring tightly integrated vector and raster data, with Natural Earth you can make a variety of visually pleasing, well-crafted maps with cartography or GIS software.

[Earth-Base](http://earth-base.org)

> Our vision for earth-base is science- and data-focused. We think of earth-base as a tetrahedron linking the solid, fluid, living earths and the rock record. This illustrates the basic principle that motivates us: earth systems are interconnected, and there is no logical “center” that should dominate this effort.

---

## Open Data

[Dryad](http://datadryad.org)

> The Dryad Digital Repository is a curated resource that makes the data underlying scientific publications discoverable, freely reusable, and citable. Dryad provides a general-purpose home for a wide diversity of datatypes.

[fig**share**](http://figshare.com)

> fig**share** is a repository where users can make all of their research outputs available in a citable, shareable and discoverable manner.

[ORNL DAAC](http://daac.ornl.gov)

> The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemcial dynamics

---

## Open Geodata Formats…

[Shapefile](http://www.esri.com/library/whitepapers/pdfs/shapefile.pdf)

> A popular geospatial vector data format for geographic information system (GIS) software. It is developed and regulated by Esri as a (mostly) open specification

[Keyhole Markup Language aka kml](http://www.opengeospatial.org/standards/kml)

> An XML notation for expressing geographic annotation and visualization within Internet-based, two-dimensional maps and three-dimensional Earth browsers.

[GeoJSON](http://geojson.org/geojson-spec.html)

> An open standard format for encoding collections of simple geographical features along with their non-spatial attributes using JavaScript Object Notation.

---

## Open Geodata Formats

[Well-Known Text](http://www.opengeospatial.org/standards/sfa)

> A text markup language for representing vector geometry objects on a map, spatial reference systems of spatial objects and transformations between spatial reference systems.

[Comma Separated Values aka x,y](http://www.ietf.org/rfc/rfc4180.txt)

> A comma-separated values (CSV) (also sometimes called character-separated values) file stores tabular data (numbers and text) in plain-text form.

[Geodatabase](http://en.wikipedia.org/wiki/ArcGIS#Geodatabase)

> An object-relational database approach for storing spatial data. A geodatabase is a "container" for holding datasets, tying together the spatial features with attributes.

---

# So, What is Open?

---

## Open: Budapest Open Access Initiative

[Budapest Open Access Initiative](http://www.budapestopenaccessinitiative.org/boai-10-recommendations)

> 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.

---

## Open: Open Definition

[Open Definition](http://opendefinition.org/)

> Open means anyone can freely access, use, modify, and share for any purpose (subject, at most, to requirements that preserve provenance and openness).

---

## Open: Free Software Foundation

[The Free Software Definition](https://gnu.org/philosophy/free-sw.html)

* The freedom to run the program as you wish, for any purpose (**freedom 0**).
* The freedom to study how the program works, and change it so it does your computing as you wish (**freedom 1**). *Access to the source code is a precondition for this.*
* The freedom to redistribute copies so you can help your neighbor (**freedom 2**).
* The freedom to distribute copies of your modified versions to others (**freedom 3*v). *By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this.*

---

## Open: Free Culture Foundation

[Free Cultural Works](http://freedomdefined.org/Definition)

* The freedom to use the work and enjoy the benefits of using it
* The freedom to study the work and to apply knowledge acquired from it
* The freedom to make and redistribute copies, in whole or in part, of the information or expression
* The freedom to make changes and improvements, and to distribute derivative works

---

## Open: Open Source Initiative

[The Open Source Definition](http://opensource.org/osd)

1. Free Redistribution
2. Source Code
3. Derived Works
4. Integrity of The Author's Source Code
5. No Discrimination Against Persons or Groups
6. No Discrimination Against Fields of Endeavor
7. Distribution of License
8. License Must Not Be Specific to a Product
9. License Must Not Restrict Other Software
10. License Must Be Technology-Neutral

---

## Open: Creative Commons

[Creative Commons License Chooser](http://creativecommons.org/choose/)

---

# It's complicated but doesn't have to be

---

## How?

Make your work **technologically**, **semantically** and **legally** open and interoperable

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## How?

### Findable

Put it on the web

### Understandable

Document it and use version control

### Usable

Remove all legal barriers to reuse

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## Make Knowledge Discovery Possible and Improve the ROI in Your Work