Add metadata about examples following OMEX Metadata guidelines

[jonrkarr]

• OMEX Meta guidelines: https://biosimulators.dev/conventions/metadata

• Complete example: https://github.com/biosimulators/Biosimulators_utils/blob/dev/tests/fixtures/omex-meta/biosimulations-with-file-annotations.rdf

• sbml-core/

  • [x] Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • [x] Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
  • [x] Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Felhberg
  • [x] Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • [x] Parmar-BMC-Syst-Biol-2017-iron-distribution
  • [x] Szymanska-J-Theor-Biol-2009-HSP-synthesis
  • [x] Tomida-EMBO-J-2003-NFAT-translocation
  • [x] Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
  • [x] Vilar-PNAS-2002-minimal-circardian-clock
  • [x] Vilar-PNAS-2002-minimal-circardian-clock-continuous (metadata is the same as Vilar-PNAS-2002-minimal-circardian-clock)
  • [x] Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (metadata is the same as Vilar-PNAS-2002-minimal-circardian-clock)
  • [x] Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (metadata is the same as Vilar-PNAS-2002-minimal-circardian-clock)

• sbml-fbc/

  • [x] Escherichia-coli-core-metabolism

• sbml-qual/

  • [x] Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling

• cellml/

  • [x] Lorenz-system

• neuroml-lems/

  • [x] Hodgkin-Huxley-cell-CVODE
  • [x] Hodgkin-Huxley-cell-Euler (annotation will be the same as for Hodgkin-Huxley-cell-CVODE)

• bngl/

  • [x] Dolan-PLoS-Comput-Biol-2015-NHEJ
  • [x] test-bngl

• smoldyn/

  • [x] Lotka-Volterra

[jonrkarr]

Instructions

• Clone this repository
• Navigate to the directory examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation. This directory contains files which describe a simulation of a model and metadata about the biology that the model represents.
• Open metadata.rdf in this directory
• We want to expand the information captured by this file and represent it in a slightly different format.
• Use https://github.com/biosimulators/Biosimulators_utils/blob/dev/tests/fixtures/omex-meta/biosimulations-with-file-annotations.rdf as a template.
• Copy information from metadata.rdf into the template.
• Gather additional information from the BioModels entry and publication for this model and copy it into the template. This information includes
  • Organism (Tetronarce californica)
  • Biology represented by the model
  • Neuromuscular synaptic transmission
  • transmission of nerve impulse
  • cell surface receptor signaling pathway
  • Thumbnail image: Figure 2 of publication
  • Citation for the publication (Edelstein SJ, Schaad O, Henry E, Bertrand D, Changeux JP. A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions. Biol. Cybern. 1996 Nov; 75(5):361-79)
• Save the modified template to metadata.rdf in the directory
• Add the thumbnail image(s) to manifest.xml in the directory, e.g.

  <content location="Figure2.png" format="http://purl.org/NET/mediatypes/image/png" master="false"/>

• Commit and push your change to the repository

  git add \
    examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf \
    examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/manifest.xml \
    examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/Figure2.png

Three additional examples include the metadata.rdf files in examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations and examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.

[jonrkarr]

@bilalshaikh42 above is an outline for Ryann. I've worked through a couple of OMEX files as examples.

[jonrkarr]

@Ryannjordan I finished this up. I'll get these examples deployed by tomorrow. You can see the corrections I made in the commit history.