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title: "OpenCitations"
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source: "https://en.wikipedia.org/wiki/OpenCitations"
category: "reference"
tags: "science, encyclopedia"
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OpenCitations (established in 2010) is a project aiming to publish open bibliographic citation information in RDF. It produces the "OpenCitations Corpus" citation database in the process.
== Datasets ==
OpenCitations publishes the following datasets which encompass bibliographic data, citation metadata, and in-text reference data. The datasets can be accessed via SPARQL, a REST API, as dumps on Figshare, as individual bibliographic entities, or using OSCAR (OpenCitations RDF Search Application) or Lucinda (The OpenCitations RDF Resource Browser).
=== OpenCitations Corpus ===
The OpenCitations Corpus (OCC) is an open repository of scholarly citation data. The repository is released under the CC0 public domain to ensure that the scholarly citation data is open to all.
As of March 19, 2022, the OCC has ingested the references from 326,743 citing bibliographic resources and contains information about 13,964,148 citation links to 7,565,367 cited resources.
=== OpenCitations Indexes ===
The OpenCitations Indexes are collections of citations, which treat citations as first-class data objects that include citation metadata, as well as identifiers to the citing and cited works. For example, COCI is the OpenCitations Index of Crossref open DOI-to-DOI citations. A 2021 comparison with other citations tools found that COCI was the smallest in coverage, and a 2020 study found that 54% of the citation links in Web of Science were also in COCI.
=== Open Biomedical Citations in Context Corpus ===
The Open Biomedical Citations in Context Corpus (CCC) is a database of citations providing in-text references, extending OpenCitations records with in-text reference pointer information.
== See also ==
Initiative for Open Citations
== References ==
== External links ==
Official website
"(OpenCitations Corpus)". Open Access Tracking Project. Harvard University. OCLC 1040261573.

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source: "https://en.wikipedia.org/wiki/OpenNeuro"
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title: "OpenWorm"
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OpenWorm is an international open science project for the purpose of simulating the roundworm Caenorhabditis elegans at the cellular level. Although the long-term goal is to model all 959 cells of the C. elegans, the first stage is to model the worm's locomotion by simulating the 302 neurons and 95 muscle cells. This bottom up simulation is being pursued by the OpenWorm community.
As of 2014, a physics engine called Sibernetic has been built for the project and models of the neural connectome and a muscle cell have been created in NeuroML format. A 3D model of the worm anatomy can be accessed through the web via the OpenWorm browser. The OpenWorm project is also contributing to develop Geppetto, a web-based multi-algorithm, multi-scale simulation platform engineered to support the simulation of the whole organism.
== Background: C. elegans ==
The roundworm Caenorhabditis elegans is a free-living, transparent nematode, about 1 mm in length, that lives in temperate soil environments. It is the type species of its genus.
C. elegans has one of the simplest nervous systems of any organism - its hermaphrodite type possesses only 302 neurons. Furthermore, the structural connectome of these neurons is fully mapped. There are fewer than one thousand cells in the whole body of a C. elegans worm, and because C. elegans is a model organism, each has a unique identifier and comprehensive supporting literature. Being a model organism, the genome is fully known, along with many well characterized mutants readily available, and a comprehensive literature of behavioural studies. With so few neurons and new 2-photon calcium microscopy techniques, it should soon be possible to record the complete neural activity of a living organism. The manipulation of neurons via optogenetic methods, in tandem with the foregoing technical capacities, has provided the project an unprecedented position - now able to fully characterize the neural dynamics of an entire organism.
The efforts to build an in silico model of C. elegans, although a relatively simple organism, have burgeoned the development of technologies that will make it easier to model progressively more complex organisms.
== OpenWorm project ==
While the ultimate goal is to simulate all features of C. elegans' behaviour, the OpenWorm community initially aimed to simulate a simple motor response: teaching the worm to crawl. To do so, the virtual worm is placed in a virtual environment. A full feedback loop is subsequently established: Environmental Stimulus > Sensory Transduction > Interneuron Firing > Motor Neuron Firing > Motor Output > Environmental Change > Sensory Transduction.
There are two main technical challenges here: modelling the neural/electrical properties of the brain as it processes the information, and modelling the mechanical properties of the body as it moves. The neural properties are being modeled by a Hodgkin-Huxley model, and the mechanical properties are being modeled by a Smoothed Particle Hydrodynamics algorithm.
The OpenWorm team built an engine called Geppetto which could integrate these algorithms and due to its modularity will be able to model other biological systems (like digestion) which the team will tackle at a later time.
The team also built an environment called NeuroConstruct which is able to output neural structures in NeuroML. Using NeuroConstruct the team reconstructed the full connectome of C. elegans.
Using NeuroML the team has also built a model of a muscle cell. Note that these models currently only model the relevant properties for the simple motor response: the neural/electrical and the mechanical properties discussed above.
The next step is to connect this muscle cell to the six neurons which synapse on it and approximate their effect.
The rough plan is to then both:
Approximate the synapses which synapse on those neurons
Repeat the process for other muscle cells
=== Progress ===
As of January 2015, the project is still awaiting peer review, and researchers involved in the project are reluctant to make bold claims about its current resemblance to biological behavior; project coordinator Stephen Larson estimates that they are "only 20 to 30 percent of the way towards where we need to get".
== Related projects ==
In 1998 Japanese researchers announced the Perfect C. elegans Project. A proposal was submitted, but the project appears to have been abandoned.
In 2004 a group from Hiroshima began the Virtual C. elegans Project. They released two papers which showed how their simulation would retract from virtual prodding.
In 2005 a Texas researcher described a simplified C. elegans simulator based on a 1-wire network incorporating a digital Parallax Basic Stamp processor, sensory inputs and motor outputs. Inputs employed 16-bit A/D converters attached to operational amplifier simulated neurons and a 1-wire temperature sensor. Motor outputs were controlled by 256-position digital potentiometers and 8-bit digital ports. Artificial muscle action was based on Nitinol actuators. It used a "sense-process-react" operating loop which recreated several instinctual behaviors.
These early attempts of simulation have been criticized for not being biologically realistic. Although we have the complete structural connectome, we do not know the synaptic weights at each of the known synapses. We do not even know whether the synapses are inhibitory or excitatory. To compensate for this the Hiroshima group used machine learning to find some weights of the synapses which would generate the desired behaviour. It is therefore no surprise that the model displayed the behaviour, and it may not represent true understanding of the system.
== Open science ==
The OpenWorm community is committed to the ideals of open science. Generally this means that the team will try to publish in open access journals and include all data gathered (to avoid the file drawer problem). Indeed, all the biological data the team has gathered is publicly available.
By mid-2024, twenty publications made by the group are available for free on their website. All the software that OpenWorm has produced is completely free and open source.
OpenWorm is also trying a radically open model of scientific collaboration. The team consists of anyone who wishes to be a part of it. There are over one hundred "members" who are signed up for the high volume technical mailing list. Of the most active members who are named on a publication there are collaborators from Russia, Brazil, England, Scotland, Ireland and the United States.
To coordinate this international effort, the team uses "virtual lab meetings" and other online tools that are detailed in the resources section.
== References ==
== External links ==
Official website
OpenWorm on GitHub
OpenWorm community
Milestones.
Sibernetic
Geppetto

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The Panton Principles are a set of principles which were written to promote open science. They were first drafted in July 2009 at the Panton Arms pub in Cambridge.
== History ==
The principles were written by Peter Murray-Rust, Cameron Neylon, Rufus Pollock, and John Wilbanks. They were then refined by the Open Knowledge Foundation and officially launched in February 2010.
== The Principles ==
1. Where data or collections of data are published it is critical that they be published with a clear and explicit statement of the wishes and expectations of the publishers concerning the re-use and re-purposing of individual data elements, the whole data collection, and subsets of the collection. This statement should be precise, irrevocable, and based on an appropriate and recognized legal statement in the form of a waiver or license.
When publishing data make an explicit and robust statement of your wishes.
2. Many widely recognized licenses are not intended for, and are not appropriate for, data or collections of data. A variety of waivers and licenses that are designed for and appropriate for the treatment of data are described here. Creative Commons licenses (apart from CCZero), GFDL, GPL, BSD, etc. are NOT appropriate for data and their use is STRONGLY discouraged.
Use a recognized waiver or license that is appropriate for data.
3. The use of licenses which limit commercial re-use or limit the production of derivative works by excluding use for particular purposes or by specific persons or organizations is STRONGLY discouraged. These licenses make it impossible to effectively integrate and re-purpose datasets and prevent commercial activities that could be used to support data preservation.
If you want your data to be effectively used and added to by others it should be open as defined by the Open Knowledge/Data Definition in particular non-commercial and other restrictive clauses should not be used.
4. Furthermore, in science it is STRONGLY recommended that data, especially where publicly funded, be explicitly placed in the public domain via the use of the Public Domain Dedication and Licence or Creative Commons Zero Waiver. This is in keeping with the public funding of much scientific research and the general ethos of sharing and re-use within the scientific community.
Explicit dedication of data underlying published science into the public domain via PDDL or CCZero is strongly recommended and ensures compliance with both the Science Commons Protocol for Implementing Open Access Data and the Open Knowledge/Data Definition.
== Response ==
Between the launch of the project and December 2011 the principles gained 150 endorsements from researchers.
One researcher said the principles allow researchers to better claim credit for their work.
The project won an innovation prize from the Scholarly Publishing and Academic Resources Coalition.
== References ==
== External links ==
Official website
video explanation of Panton Principles
Murray-Rust, Peter (16 May 2009). "Unilever Centre for Molecular Informatics, Cambridge - The Panton Principles: A breakthrough on data licensing for public science?". blogs.ch.cam.ac.uk. Retrieved 26 June 2013.

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title: "Polymath Project"
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source: "https://en.wikipedia.org/wiki/Polymath_Project"
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The Polymath Project is a collaboration among mathematicians to solve important and difficult mathematical problems by coordinating many mathematicians to communicate with each other on finding the best route to the solution. The project began in January 2009 on Timothy Gowers's blog when he posted a problem and asked his readers to post partial ideas and partial progress toward a solution. This experiment resulted in a new answer to a difficult problem, and since then the Polymath Project has grown to describe a particular crowdsourcing process of using an online collaboration to solve any math problem.
== Origin ==
In January 2009, Gowers chose to start a social experiment on his blog by choosing an important unsolved mathematical problem and issuing an invitation for other people to help solve it collaboratively in the comments section of his blog. Along with the math problem itself, Gowers asked a question which was included in the title of his blog post, "is massively collaborative mathematics possible?" This post led to his creation of the Polymath Project.
== Projects for high school and college ==
Since its inception, it has now sponsored a "Crowdmath" project in collaboration with MIT PRIMES program and the Art of Problem Solving. This project is built upon the same idea of the Polymath Project that massive collaboration in mathematics is possible and possibly quite fruitful. However, this is specifically aimed at only high school and college students with a goal of creating "a specific opportunity for the upcoming generation of math and science researchers." The problems are original research and unsolved problems in mathematics. All high school and college students from around the world with advanced background of mathematics are encouraged to participate. Older participants are welcomed to participate as mentors and encouraged not to post solutions to the problems. The first Crowdmath project began on March 1, 2016.
== Problems solved ==
=== Polymath1 ===
The initial proposed problem for this project, now called Polymath1 by the Polymath community, was to find a new combinatorial proof to the density version of the HalesJewett theorem. As the project took form, two main threads of discourse emerged. The first thread, which was carried out in the comments of Gowers's blog, would continue with the original goal of finding a combinatorial proof. The second thread, which was carried out in the comments of Terence Tao's blog, focused on calculating bounds on density of HalesJewett numbers and Moser numbers for low dimensions.
After seven weeks, Gowers announced on his blog that the problem was "probably solved", though work would continue on both Gowers's thread and Tao's thread well into May 2009, some three months after the initial announcement. In total over 40 people contributed to the Polymath1 project. Both threads of the Polymath1 project have been successful, producing at least two new papers to be published under the pseudonym D. H. J. Polymath, where the initials refer to the problem itself (density HalesJewett).
=== Polymath5 ===
This project was set up in order to try to solve the Erdős discrepancy problem. It was active for much of 2010 and had a brief revival in 2012, but did not end up solving the problem. However, in September 2015, Terence Tao, one of the participants of Polymath5, solved the problem in a pair of papers. One paper proved an averaged form of the Chowla and Elliott conjectures, making use of recent advances in analytic number theory concerning correlations of values of multiplicative functions. The other paper showed how this new result, combined with some arguments discovered by Polymath5, were enough to give a complete solution to the problem. Thus, Polymath5 ended up making a significant contribution to the solution.
=== Polymath8 ===
The Polymath8 project was proposed to improve the bounds for small gaps between primes. It has two components:
Polymath8a, "Bounded gaps between primes", was a project to improve the bound H = H1 on the least gap between consecutive primes that was attained infinitely often, by developing the techniques of Yitang Zhang. This project concluded with a bound of H = 4,680.
Polymath8b, "Bounded intervals with many primes", was a project to improve the value of H1 further, as well as Hm (the least gap between primes with m-1 primes between them that is attained infinitely often), by combining the Polymath8a results with the techniques of James Maynard. This project concluded with a bound of H = 246, as well as additional bounds on Hm.
Both components of the Polymath8 project produced papers in 2014, one of which was published under the pseudonym D. H. J. Polymath.

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title: "Polymath Project"
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---
== Publications ==
Polymath, D. H. J. (2010), "Density Hales-Jewett and Moser numbers", An irregular mind, Bolyai Soc. Math. Stud., vol. 21, János Bolyai Math. Soc., Budapest, pp. 689753, arXiv:1002.0374, doi:10.1007/978-3-642-14444-8_22, ISBN 978-3-642-14443-1, MR 2815620, S2CID 15547977. From the Polymath1 project.
Polymath, D. H. J. (2012), "A new proof of the density Hales-Jewett theorem", Annals of Mathematics, Second Series, 175 (3): 12831327, arXiv:0910.3926, doi:10.4007/annals.2012.175.3.6, MR 2912706, S2CID 60078. From the Polymath1 project.
Tao, Terence; Croot, Ernest III; Helfgott, Harald (2012), "Deterministic methods to find primes", Mathematics of Computation, 81 (278): 12331246, arXiv:1009.3956, doi:10.1090/S0025-5718-2011-02542-1, MR 2869058. From the Polymath4 project. Although the journal editors required the authors to use their real names, the arXiv version uses the Polymath pseudonym.
Polymath, D. H. J. (2014), "New equidistribution estimates of Zhang type", Algebra & Number Theory, 9 (8): 20672199, arXiv:1402.0811, Bibcode:2014arXiv1402.0811P, doi:10.2140/ant.2014.8.2067. From the Polymath8 project.
Polymath, D.H.J. (2014), "Variants of the Selberg sieve, and bounded intervals containing many primes", Research in the Mathematical Sciences, 1 (12) 12, arXiv:1407.4897, Bibcode:2014arXiv1407.4897P, doi:10.1186/s40687-014-0012-7, MR 3373710, S2CID 119699189 From the Polymath8 project.
Polymath, D. H. J. (2014), "The "bounded gaps between primes" Polymath project: A retrospective analysis" (PDF), Newsletter of the European Mathematical Society, 94: 1323, arXiv:1409.8361, Bibcode:2014arXiv1409.8361P.
Polymath, D. H. J. (2018), "Homogeneous length functions on groups", Algebra & Number Theory, 12 (7): 17731786, arXiv:1801.03908, doi:10.2140/ant.2018.12.1773, MR 3871510. From the Polymath14 project. The journal and arXiv versions use the Polymath pseudonym, though the author names appear in the journal's table of contents and on the DOI page.
Polymath, D. H. J. (2019), "Effective approximation of heat flow evolution of the Riemann $\xi$ function, and a new upper bound for the de Bruijn-Newman constant", Research in the Mathematical Sciences, 6 (3) 31: 67 pp. (paper no. 31), arXiv:1904.12438, doi:10.1007/s40687-019-0193-1, MR 4011563. From the Polymath15 project.
== See also ==
Citizen science
Crowdsourcing
== References ==
== Bibliography ==
Barany, Michael J. (2010). "'[B]ut this is blog maths and we're free to make up conventions as we go along': Polymath1 and the modalities of 'massively collaborative mathematics'". Proceedings of the 6th International Symposium on Wikis and Open Collaboration (WikiSym '10). New York: ACM. Article 10. doi:10.1145/1832772.1832786. ISBN 978-1-4503-0056-8. S2CID 17903199.
Cranshaw, Justin; Kittur, Aniket (2011). "The polymath project: lessons from a successful online collaboration in mathematics". Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI '11). New York: ACM. pp. 186574. doi:10.1145/1978942.1979213. ISBN 978-1-4503-0228-9. S2CID 2498854.
Stefaneas Petros, Vandoulakis Ioannis "The Web as a Tool for Proving", Metaphilosophy. Special Issue: Philoweb: Toward a Philosophy of the Web. Guest Editors: Harry Halpin and Alexandre Monnin. Volume 43, Issue 4, pp 480498, July 2012, DOI: 10.1111/j.1467-9973.2012.01758.x http://web-and-philosophy.org. Reprinted in the collection: Harry Halpin and Alexandre Monnin (Eds) Philosophical Engineering: Toward a Philosophy of the Web. Wiley-Blackwell, 2014, 149167. DOI: 10.1002/9781118700143.ch10
== External links ==
Current central hub of the Polymath Project
Polymath Project blog
Gowers's blog post inspiring the project
An introduction to the Polymath Project for non-mathematicians

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title: "Preprints.org"
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source: "https://en.wikipedia.org/wiki/Preprints.org"
category: "reference"
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---
Preprints.org is an open-access platform of electronic preprints approved for posting after moderation. Research in various areas can be posted as preprints on Preprints.org, including manuscripts from all fields of research.
Preprints was established by MDPI in 2016. As of March 2026, Preprints.org contains more than 124,000 preprints.
== Abstracting and indexing ==
As of May 2023, preprints posted on Preprints.org appear in:
Web of Science (Preprint Citation Index)
Europe PMC
Crossref
Google Scholar
PrePubMed
Portico
== See also ==
List of academic databases and search engines
List of academic journals by preprint policy
Open-access repository
List of preprint repositories
== References ==

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source: "https://en.wikipedia.org/wiki/PubPeer"
category: "reference"
tags: "science, encyclopedia"
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title: "PubRef.org"
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source: "https://en.wikipedia.org/wiki/PubRef.org"
category: "reference"
tags: "science, encyclopedia"
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---
PubRef.org was a short lived project that is now discontinued.
The website is not accessible anymore. An old version can be accessed from the Internet Archive.
They used the same name PubRef which was a service provided by PubMed for linking bibliographies, defeated by the independent service Crossref.
PubRef was a composition and project management application used by researchers and students for scholarly writing and communication.
PubRef uses an extended form of Markdown as a primary authoring format and converts this to JATS, the archive format used by the US National Library of Medicine.
== Research asset containerization ==
Researchers manage scholarly writing projects within version-controlled file repositories called containers that function similarly to git repositories and docker containers to provide enhanced reproducibility, transparency and re-usability in digital science publishing.
== Manuscript writing ==
A PubRef manuscript is a Markdown file within a container that contains extra embedded information that describes the essential front matter elements of a scholarly manuscript such as the title, short title, list of authors, author affiliations, key words. This information is captured in embedded YAML blocks within the primary manuscript called Meta. Figures, tables, equations and other special content can be similarly embedded within the context of the document via Meta descriptors.
== Minimal example ==
This minimal formatting example repurposes a classic paper by Stephen Hawking and Roger Penrose The Singularities of Gravitational Collapse and Cosmology:
# Introduction
An important feature of gravitation, for very large concentrations of mass, is that it is essentially *unstable*. This is due...
== Manuscript publishing ==
Once the essential frontmatter meta elements have been declared, manuscripts can be automatically submitted to academic publishers.
Articles, supporting data, and dependent code can be published directly on PubRef in the form of personal communications under the DOI prefix 10.17920/P9.pubref.
== References ==

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title: "Registry of Research Data Repositories"
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source: "https://en.wikipedia.org/wiki/Registry_of_Research_Data_Repositories"
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The Registry of Research Data Repositories (re3data.org) is an open science tool that offers researchers, funding organizations, libraries, and publishers an overview of existing international repositories for research data.
== Background ==
re3data.org is a global registry of research data repositories from all academic disciplines. It provides an overview of existing research data repositories in order to help researchers to identify a suitable repository for their data and thus comply with requirements set out in data policies.
The registry went live in autumn 2012.
== Content ==
In 2023 the registry lists over 3000 research data repositories from around the world covering all academic disciplines. They are described in detail using the re3data.org schema.
The service makes all metadata in the registry available for open use under the Creative Commons deed CC0.
== Features ==
The majority of the listed research data repositories are described in detail by a comprehensive schema, namely the re3data.org Schema for the Description of Research Data Repositories.
Information icons support researchers to identify an adequate repository for the storage and reuse of their data.
== Inclusion criteria ==
A repository is indexed when the minimum requirements for inclusion in re3data.org are met: the repository has to be run by a legal entity, such as a sustainable institution (e.g., library, university) and clearly state access conditions to the data and repository as well as the terms of use. Additionally, an English graphical user interface (GUI) plus a focus on research data is needed.
== Partners and cooperation ==
re3data.org was initiated as a joint project funded by the German Research Foundation (DFG).
Current partners in re3data are DataCite, the Berlin School of Library and Information Science at the Humboldt-Universität zu Berlin, the Helmholtz Open Science Office of the Helmholtz Association, the KIT Library at the Karlsruhe Institute of Technology (KIT) and the Libraries of the Purdue University.
Several publishers, research institutions and funders refer to re3data.org in their editorial policies and guidelines as a tool for the identification of suitable data repositories, such as Springer Nature the European Commission or the National Science Foundation (NSF).
== See also ==
Data curation
Data sharing
Scientific data archiving
== References ==
== External links ==
Official website