Polish metadata

[jonrkarr]

I looked at the metadata that's been assembled (https://github.com/biosimulations/biosimulations-physiome/blob/dev/projects.json). It looks pretty good. It looks like a few attributes need to be transformed for BioSimulators-utils and a couple of additional pieces of information could be scraped (markdown formatting for description, license, timestamp from Git commit)

• [x] identifier:
  • Because of the two namespaces (e and exposure), I think the identifiers need to be e/xxx or exposure/xxxxxxxxxxxxxx
  • BioSimulators-utils utils expects the key to be identifiers rather than identifier.
  • BioSimulators-utils utils expects the value to be a list of dictionaries with keys
  • uri: http://identifiers.org/pmr:e/xxx
  • label: pmr:e/xxx
• [x] hash: FYI, BioSimulators-utils will ignore this. The hash could be encoded into the source. See next bullet.
• [x] source:
  • BioSimulators-utils expects this key to be sources rather than source
  • BioSimulators-utils expects the value to be a dictionary with two keys
  • uri: http://identifiers.org/pmr.workspace:35f/@@file/81ef7ed4cf06f0cd4b87da239d282fc559738796 (I think the hash could be encoded here; I just requested a identifiers.org prefix for this)
  • label: pmr.workspace:35f/@@file/81ef7ed4cf06f0cd4b87da239d282fc559738796
• [x] title: Looks good

• [x] description: Markdown can be used to capture the formatting. Here's a sketch of how it can be done

  import bs4
  import markdownify
  import requests
  
  response = requests.get('https://models.physiomeproject.org/e/3fd')
  response.raise_for_status()
  html = response.content
  
  doc = bs4.BeautifulSoup(html)
  content_core = doc.find(id='content-core').find('div')
  for table in content_core.find_all(class_='tmp-doc-informalfigure table'):
      table.decompose()
  for image in content_core.find_all('img'):
      image.decompose()
  
  description = markdownify.MarkdownConverter().convert_soup(content_core).strip()

• [x] summary: empty strings ("") should be converted to null
• [x] thumbnails: For BioSimulators-utils, the thumbnails will need to be downloaded and the values of the thumbnails attribute will need to be converted to a path within the COMBINE archive (i.e. strip off everything up to the identifier)
• [x] tags:
  • BioSimulators-utils expects this key to be keywords rather than tags
  • BioSimulators-utils expects the value of this key to be a list of strings
• [x] citation
  • BioSimulators-utils expects this key to be references rather than citation
  • BioSimulators-utils expects the value to be a list of dictionaries with keys
  • uri: http://identifiers.org/pubmed/19486676
  • label: An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis. .... This method can be used to look up more complete metadata and generate a human-readable label for references https://github.com/biosimulators/Biosimulators_utils/blob/f8370913679828b6a45dad047123c0ab84a6f43d/biosimulators_utils/ref/utils.py#L23.
• [x] authors: BioSimulators-utils expects authors to be a list of dictionaries with keys
  • uri: null (preferably this would be ORCIDs, but we don't know these)
  • label: e.g., Geoffrey Nunns
• [x] contributors: BioSimulators-utils expects contributors to be a list of dictionaries with keys
  • uri: http://identifiers.org/orcid:0000-0001-5801-5510 (preferably ORCID, another URI is fine too such as your personal website, GitHub profile, etc.)
  • label: Bilal Shaikh
• [x] license:
  • I think we should scrape this because people care about preserving license information.
  • Most, but not all models are licensed CC BY 3.0. I think we need to scrape this from the web pages. Some pages say The terms of use/license for this work is unspecified. (i.e., "license": null). Some pages don't say anything about licenses, which I guess we can interpret as "license": null.
  • I think you could scrape this text from each model, calculate the set of unique strings (possibly as small as 2), and then assign each to the appropriate SPDX id.
  • BioSimulators-utils expects the license to be captured as a dictionary with two keys
  • uri: http://identifiers.org/spdx:CC-BY-3.0
  • label: CC BY 3.0
• [ ] created: I think this could be set equal to the timestamp for the git commit.

[jonrkarr]

Replaced with other issues

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