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Communal methods and links to sub-projects using OpenNotebookScience
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openNotebook launched at elifeSprint Cambridge 2019

This toplevel resurce supports both the general concept of literature-based OpenNoteBook Science and also 3 specific projects (climate, plant oils, computational chemistry). For anyone at the sprint this is the first place to come. We will also use the Issues to create a general discourse and report errors.


This site is dedicated to Jean-Claude Bradley (v.i.), and also to my father (David Murray-Rust) headmaster at Sidcot School for 11 years. David gave me a love of science, teaching and collaboration. My brother Hammond is giving the Darwen lecture in 2 weeks time and I'll introduce the climate part of this site to the school then and invite collaboration.

Opennotebook science

The term "OpenNotebookScience" (ONS) was conceived and popularised by Jean-Claude Bradley. This site is jointly dedicated to him. Jean-Claude showed that can and almost always should be fully Open, where everything is visible on the public web as soon as it is created (i.e. within minutes). J-C's phrase was "no insider knowledge", i.e. everybody reading the site can know what experiments, data, discourse, computation has taken place. It may or may not mean that anyone can take part. In this OpenNoteBook everyone can, in principle, take part but they need a basic knowledge of the technology, and a collaborative approach, with a certain amount of discipline and will need to be invited to be part of the repo.

motivation for this site

Catalyzed by three projects but adaptable to any subject with open access papers and an enthusiastic community:

quantum chemistry

Leonie Mueck suggested this topic for the eLifeSprint in Cambridge 20190904. PMR emphasis in QChem is computation of chemical properties (mainly molecules and crystals) using Schroedinger's equation. (BTW QChem is used to compute the properties of many biological molecules, including proteins and nucleic acids so it's mainstream bioscience!)

See which has a good example of how to create a dictionary from Wikipedia page.

(20190912: This is currently on hold - until Leonie wants to re-activate.)

climate change

PeterMR and Simon Worthington met virtually and are creatin a shared OpenScience project for mining papers on climate chane - EPMC has > 65K open access papers.

See which has a good example of how to create a dictionary of 230+ terms from Wikipedia page.

(climate is critically part of bioscience!)

medicinal plants

Work with Gita Yadav (NIPGR India and Cambridge) and Emanuel Faria (Verriclear) on essential oils and their reported activities.

See which will use recent semantic plant and chemical dictionaries from the EssoilDB project in NIPGR..

shared resources

These projects will all be using the same resources and so documentation can be done here and shared.


The tools were developed for and used in the TIGR2ESS workshop in New Delhi 20190228. We'll often point to the tutorials there, but rememebr they were developedfor a particular, real-life, occasion and a specific subject (crops (rice, wheat, millets)).


Tutorial from Vinita Lamba. Shows what EPMC does, how to search it manually.

ContentMine software

ContentMine has two main tools, the first for searching/downloading; the second for analysing


Tutorial from Ambarish Kuamr. Shows how to automatically search and download from EPMC.


Tutorial from Amit Yadav. Start here to analyze downloaded papers.


Tutorial on dictionary structure, how to create them manually and programmatically from lists and pages, especially Wikipedia.


Wikipedia rather truncated.

Wikidata introduction.

WikiFactMine ContentMine's dictionaries created from Wikidata, and searchable via SPARQL.

XML for Openscience

I am presenting CEV to XML Summerschool in Oxford 2019-09-18 and will use medicinal plants as examples. I have therefore separated the XML technology into XML for Open Science

other tools


Crossref holds metadata on "every" published article submmited by publishers (but not theses, etc.). This normally holds a DOI which can be used to find the article on a publisher's site (or through Unpaywall). Crossref resources


Unpaywall holds the addresses and metadata of "most" articles which are "freely available legally". This is a difficult task and depends on getting metadata from repositories and other sites that hold them. Unpaywall resources

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