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Mike Chelen

Open Knowledge Foundation Blog » Blog Archive » Open Data: Openness and Licen... - 0 views

  • Why bother about openness and licensing for data
  • It’s crucial because open data is so much easier to break-up and recombine, to use and reuse.
  • want people to have incentives to make their data open and for open data to be easily usable and reusable
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  • good definition of openness acts as a standard that ensures different open datasets are ‘interoperable’
  • Licensing is important because it reduces uncertainty. Without a license you don’t know where you, as a user, stand: when are you allowed to use this data? Are you allowed to give to others? To distribute your own changes, etc?
  • licensing and definitions are important even though they are only a small part of the overall picture
  • If we get them wrong they will keep on getting in the way of everything else.
  • Everyone agrees that requiring attribution is OK
    • Mike Chelen
       
      My opinion is that there should be no requirements, including attribution, and that standards should be community-based instead of legal.
  • Even if a basic license is used it can be argued that any ‘requirements’ for attribution or share-alike should not be in a license but in ‘community norms’.
    • Mike Chelen
       
      Licenses and community norms are not exclusive. It's recommended to adopt a Public Domain license, and encourage attribution through community standards.
  • A license is likely to elicit at least as much, and almost certainly more, conformity with its provisions than community norms.
    • Mike Chelen
       
      Ease of access and should be the goal, not conformity.
  • (even to a user it is easy to comply with the open license)
    • Mike Chelen
       
      It is important to specifically publish using a Public Domain dedication.
  •  
    Why bother about openness and licensing for data? After all they don't matter in themselves: what we really care about are things like the progress of human knowledge or the freedom to understand and share.
Mike Chelen

Protocol for Implementing Open Access Data - 0 views

  • information for the Internet community
  • distributing data or databases
  • “open” and “open access”
  • ...69 more annotations...
  • requirements for gaining and using the Science Commons Open Access Data Mark and metadata
  • interoperability of scientific data
  • terms and conditions around data make integration difficult to legally perform
  • single license
  • data with this license can be integrated with any other data under this license
  • too many databases under too many terms already
  • unlikely that any one license or suite of licenses will have the correct mix of terms
  • principles for open access data and a protocol for implementing those principles
  • Open Access Data Mark and metadata
  • databases and data
  • the foundation to legally integrate a database or data product
  • another database or data product
  • no mechanisms to manage transfer or negotiations of rights unrelated to integration
  • submitted to Science Commons for certification as a conforming implementation
  • Open Access Data trademarks (icons and phrases) and metadata on databases
  • protocol must promote legal predictability and certainty
  • easy to use and understand
  • lowest possible transaction costs on users
  • Science Commons’ experience in distributing a database licensing Frequently Asked Questions (FAQ) file
  • hard to apply the distinction between what is copyrightable and what is not copyrightable
  • lack of simplicity restricts usage
  • reducing or eliminating the need to make the distinction between copyrightable and non-copyrightable elements
  • satisfy the norms and expectations of the disciplines providing the database
  • norms for citation will differ
  • norms must be attached
  • Converge on the public domain by waiving all rights based on intellectual property
  • reconstruction of the public domain
  • scientific norms to express the wishes of the data provider
  • public domain
  • waiving the relevant rights on data and asserting that the provider makes no claims on the data
  • Requesting behavior, such as citation, through norms rather than as a legal requirement based on copyright or contracts, allows for different scientific disciplines to develop different norms for citation.
  • waive all rights necessary for data extraction and re-use
  • copyright
  • sui generis database rights
  • claims of unfair competition
  • implied contracts
  • and other legal rights
  • any obligations on the user of the data or database such as “copyleft” or “share alike”, or even the legal requirement to provide attribution
  • non-legally binding set of citation norms
  • waiving other statutory or intellectual property rights
  • there are other rights, in addition to copyright, that may apply
  • uncopyrightable databases may be protected in some countries
  • sui generis rights apply in the European Union
  • waivers of sui generis and other legal grounds for database protection
  • no contractual controls
  • using contract, rather than intellectual property or statutory rights, to apply terms to databases
  • affirmatively declare that contractual constraints do not apply to the database
  • interoperation with databases and data not available under the Science Commons Open Access Data Protocol through metadata
  • data that is not or cannot be made available under this protocol
  • owner provides metadata (as data) under this protocol so that the existence of the non-open access data is discoverable
  • digital identifiers and metadata describing non-open access data
  • “Licensing” a database typically means that the “copyrightable elements” of a database are made available under a copyright license
  • Database FAQ, in its first iteration, recommended this method
  • recommendation is now withdrawn
  • copyright begins in and ends in many databases
  • database divided into copyrightable and non copyrightable elements
  • user tends to assume that all is under copyright or none is under copyright
  • share-alike license on the copyrightable elements may be falsely assumed to operate on the factual contents of a database
  • copyright in situations where it is not necessary
  • query across tens of thousands of data records across the web might return a result which itself populates a new database
  • selective waiving of intellectual property rights fail to provide a high degree of legal certainty and ease of use
  • problem of false expectations
  • apply a “copyleft” term to the copyrightable elements of a database, in hopes that those elements result in additional open access database elements coming online
  • uncopyrightable factual content
  • republish those contents without observing the copyleft or share-alike terms
  • cascading attribution if attribution is required as part of a license approach
  • Would a scientist need to attribute 40,000 data depositors in the event of a query across 40,000 data sets?
  • conflict with accepted norms in some disciplines
  • imposes a significant transaction cost
Mike Chelen

opentextbooks - Open Knowledge Foundation Wiki - 0 views

  • Rick_GTP Rick Watson, Global Text Project and University of Georgia
  • ameeg Amee Godwin, ISKME, OER Commons, Calif
  • jwyg jwyg = Jonathan Gray, The Open Knowledge Foundation + Open Text Book
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  • karen_at_k12opened Karen Fasimpaur from K12 Opened and the Kids Open Dictionary (http://dictionary.k12opened.com)
  • JudyBaker Judy Baker, Director of Community College Open Textbook and Dean of Foothill Global Access, Foothill College, California
  • jonathan_Connexions Jonathan Emmons, community development specialist for the Connexions Project
  • Don Don McCubbrey, University of Denver, Co-Project leader if Global Text (http://globaltext.org) with Rick Watson
  • emerika Brad Emerson K12 Opened.com and the Kids Open Dictionary
  • JudyBaker Community College Consortium for Open Educational Resources (http://cccoer.wordpress.org)
  • mikechelen Mike Chelen, OpenSci.Info
  • Andrew Andrew Whitworth, English Wikibooks
  • sub Sub, (french) admin and main contributor to http://fr.wikibooks.org/
  • mib_9pubxh Sanford Forte, Senior Research and Project Consultant, Community College Open Textbook Project; and, Founder/Director, California open Source Textbook Project
  • mpal Yes, this is Murugan
  • mpal from CK-12 Foundation
Mike Chelen

Science 2.0 - introduction and perspectives for Poland « Freelancing science - 0 views

  • transcript of Science 2.0 based on a presentation I gave on conference on open science organized in Warsaw earlier this month
  • prepared for mixed audience and focused on perspectives for Poland
  • new forms of communication between scientists
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  • research become meaningful only after confronting results with the scientific community
  • peer-reviewed publication is the best communication channel we had so far
  • new communication channels complement peer-reviewed publication
  • two important attributes in which they differ from traditional models: openness and communication time
  • increased openness and shorter communication time happens already in publishing industry (via Open Access movement and experiments with alternative/shorter ways of peer-review)
  • say few words about experiments that go little or quite a lot beyond publication
  • My Experiment as an example of an important step towards openness
  • least radical idea you can find in modern Science 2.0 world
  • virtual research environment
  • focus is put on sharing scientific workflows
  • use case
  • diagram of the “methods” sections from experimental (including bioinformatics analyses) publications
  • make it easier for others to understand what we did
  • can open towards other scientists we can also open towards non-experts
  • people from all over the world compete in improving structural models of proteins
  • helps in improving protein structure prediction software and in understanding protein folding
  • combine teaching and data annotation
  • metagenome sequences in first case and chemistry spectra in the second
  • interactive visualizations of chemical structures, genomes, proteins or multidimensional data
  • communicate some difficult concepts faster
  • new approaches in conference reporting
  • report in real time from the conference
  • followed by a number of people, including even the ones that were already on the conference
  • “open notebook science” which means conducting research using publicly available, immediately updated laboratory notebook
  • The reason I did a model for Cameron’s grant was that I subscribed to his feed before
  • I didn’t subscribe to Cameron because I knew his professional profile
  • I read his blog, I commented on it and he commented on mine, etc.
  • participation in online communities
  • important part of Science 2.0 is the fact that it has human face
  • PhDs about the same time
  • first was from a major Polish institute, the second from a major European one
  • what a head of a lab both would apply to will see
  • gap we must fill, this is between current research and lectures we give today
  • access to real-time scientific conversation
  • follow current research and decide what is important to learn
  • synthetic biology
  • not all universities in world have synthetic biology courses
  • didn’t stop these students, and they plan to participate in IGEM again
  • not only scientists – there are librarians, science communicators, editors from scientific journals, people working in biotech industry
  • community of life scientists
  • even people without direct connection to science
  • diverse skills and background
  • online conference
  • interact with them and to learn from them
Mike Chelen

Main Page - Open Bioinformatics Foundation - 0 views

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    The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics. The foundation grew out of the volunteer projects BioPerl, BioJava and BioPython and was formally incorporated in order to handle our modest requirements of hardware ownership, domain name management and funding for conferences and workshops.The Foundation does not participate directly in the development or structure of the open source work, but as the members of the foundation are drawn from the member projects, there is clear commonality of direction and purpose. Occasionally the O|B|F directors may make announcements about our direction or purpose (a recent one was on the licensing of academic software) when the board feels there is a need to clarify matters, but in general we prefer to remain simply the administrative support organization for our member projects. Our main activities are: * Underwriting and supporting the BOSC conferences * Organizing and supporting developer-centric "hackathon" events * Managing our servers, colocation facilities, bank account & other assets We are incorporated in the state of Delaware, USA as a not-for-profit company.
Mike Chelen

Open Knowledge Foundation Blog » Blog Archive » Comments on the Science Commo... - 0 views

  • the protocol does not discuss any of the possible attractions of allowing such provisions
  • Protocol gives 3 basic reasons for preferring the ‘PD’ approach
  • Science Commons Protocol for Implementing Open Access Data
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  • I am not really convinced by any of these points that attribution or share-alike provisions should not be included in open data licenses
  • application of obligations based on copyright in situations where it is not necessary
  • non-copyrightable elements extends to the entire database and inadvertently infringe
  • If intellectual property rights are involved
  • requirements carrying a stiff penalty for failure
  • selective waiving of intellectual property rights
  • interpretative problems
Mike Chelen

The National Center for Biomedical Ontology - 0 views

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    The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods allowing scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our visionis that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that they are semantically interoperable and useful for improving biomedical science and clinical care. Our resources include the Open Biomedical Ontologies (OBO) library, the Open Biomedical Data (OBD) repositories, and tools for accessing and using this information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects to enable outside research and stimulate technology development in the Center. The Center undertakes outreach and educational activities (Biomedical Informatics Program) to train future researchers to use biomedical ontologies and related tools with the goal of enhancing scientific discovery.
Mike Chelen

OPENCV \ library - 0 views

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    OpenCV is an open source computer vision library originally developed by Intel. It is free for commercial and research use under a BSD license. The library is cross-platform, and runs on Mac OS X, Windows and Linux. It focuses mainly towards real-time image processing, as such, if it finds Intel's Integrated Performance Primitives on the system, it will use these commercial optimized routines to accelerate itself. This implementation is not a complete port of OpenCV. Currently, this library supports : * real-time capture * video file import * basic image treatment (brightness, contrast, threshold, …) * object detection (face, body, …) * blob detection Future versions will include more advanced functions such as motion analysis, object and color tracking, multiple OpenCV object instances … For more information about OpenCV visit the Open Source Computer Vision Library Intel webpage, the OpenCV Library Wiki, and the OpenCV Reference Manual (pdf).
Mike Chelen

BioLit Project - 0 views

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    The establishment of open access literature makes it possible for knowledge to be extracted from scholarly articles and included in other resources. BioLit aims to extract database identifiers and rich meta-data from open access articles in the life sciences and integrate that information with existing biological databases. We have begun prototyping this effort using a clone of the RCSB Protein Data Bank, a database of macromolecular structures.
Mike Chelen

Resources - ccLearn - 0 views

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    ccLearn is always on the look out for helpful and informative media championing the strengths of open educational resources. If you know of a good OER resource, helpful article, or interesting video, please let us know and we will examine it for inclusion. This page is constantly being updated, so be sure to come back and check out the latest information on open education.
Mike Chelen

Science in the open » A breakthrough on data licensing for public science? - 0 views

  • Peter Murray-Rust and others at the Unilever Centre for Molecular Informatics at Cambridge
  • conversation we had over lunch with Peter, Jim Downing, Nico Adams, Nick Day and Rufus Pollock
  • appropriate way to license published scientific data
  • ...27 more annotations...
  • value of share-alike or copyleft provisions of GPL and similar licenses
  • spreading the message and use of Open Content
  • prevent “freeloaders” from being able to use Open material and not contribute back to the open community
  • presumption in this view is that a license is a good, or at least acceptable, way of achieving both these goals
  • allow people the freedom to address their concerns through copyleft approaches
  • Rufus
  • concerned more centrally with enabling re-use and re-purposing of data as far as is possible
  • make it easy for researchers to deliver on their obligations
  • worried by the potential for licensing to make it harder to re-use and re-mix disparate sets of data and content into new digital objects
  • “license”, will have scientists running screaming in the opposite direction
  • we focused on what we could agree on
  • common position statement
  • area of best practice for the publication of data that arises from public science
  • there is a window of opportunity to influence funder positions
  • data sharing policies
  • “following best practice”
  • don’t tend to be concerned about freeloading
  • providing clear guidance and tools
  • if it is widely accepted by their research communities
  • “best practice is X”
  • enable re-use and re-purposing of that data
  • share-alike approaches as a community expectation
  • Explicit statements of the status of data are required and we need effective technical and legal infrastructure to make this easy for researchers.
  • “Where a decision has been taken to publish data deriving from public science research, best practice to enable the re-use and re-purposing of that data, is to place it explicitly in the public domain via {one of a small set of protocols e.g. cc0 or PDDL}.”
  • focuses purely on what should be done once a decision to publish has been made
  • data generated by public science
  • describing this as best practice it also allows deviations that may, for whatever reason, be justified by specific people in specific circumstances
Mike Chelen

SourceForge.net: CloudBurst - cloudburst-bio - 0 views

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    CloudBurst: Highly Sensitive Short Read Mapping with MapReduce Michael Schatz Center for Bioinformatics and Computational Biology, University of Maryland Next-generation DNA sequencing machines are generating an enormous amount of sequence data, placing unprecedented demands on traditional single-processor read mapping algorithms. CloudBurst is a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. It is modeled after the short read mapping program RMAP, and reports either all alignments or the unambiguous best alignment for each read with any number of mismatches or differences. This level of sensitivity could be prohibitively time consuming, but CloudBurst uses the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. CloudBurst's running time scales linearly with the number of reads mapped, and with near linear speedup as the number of processors increases. In a 24-processor core configuration, CloudBurst is up to 30 times faster than RMAP executing on a single core, while computing an identical set of alignments. In a large remote compute clouds with 96 cores, CloudBurst reduces the running time from hours to mere minutes for typical jobs involving mapping of millions of short reads to the human genome. CloudBurst is available open-source as a model for parallelizing other bioinformatics algorithms with MapReduce.
Mike Chelen

Welcome to BioConductor - bioconductor.org - 0 views

shared by Mike Chelen on 12 Dec 08 - Cached
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    bioconductor.org Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
Mike Chelen

open science blog - 0 views

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    The Network for Open Scientific Innovation is founded upon the belief, no, the unshakeable certainty, that creativity, love, and intelligence can solve any problem. Recent years have seen technological revolutions in informatics, communications, and the life sciences. Sadly, this rapid progress has not been matched by a revolution in the democratization of scientific problem solving.
Mike Chelen

Directory of open access journals - 0 views

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    Welcome to the Directory of Open Access Journals. This service covers free, full text, quality controlled scientific and scholarly journals. We aim to cover all subjects and languages. There are now 3768 journals in the directory. Currently 1327 journals are searchable at article level. As of today 240018 articles are included in the DOAJ service.
Mike Chelen

SourceForge.net: Open Computer Vision Library - 0 views

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    The Open Computer Vision Library has > 500 algorithms, documentation and sample code for real time computer vision. Tutorial documentation is in O'Reilly Book: Learning OpenCV http://www.amazon.com/Learning-OpenCV-Computer-Vision-Library/dp/0596516134
Mike Chelen

Open Journal Systems | Public Knowledge Project - 0 views

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    Open Journal Systems (OJS) is a journal management and publishing system that has been developed by the Public Knowledge Project through its federally funded efforts to expand and improve access to research.
Mike Chelen

DRIVER Wiki | Main / DRIVER Wiki Home Page - 0 views

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    The purpose of this wiki is to provide a home for community contributions from across Europe, to create a dynamic and updatable picture of open access activity in the EU.
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