Collection metadata UI and backend
Updated 10 Nov by @lathrops1 to address Coko questions
Updated 8 Nov for NCBI review
Workflow for collection metadata
See flow diagram in #678 (closed) and the related Collection-meta sheet.
NCBI has provided these samples:
- Column B in sheet: Sample COLLECTION.XML bookhelpcollect.xml bookiarcmonocollect.xml
- Sample
<book>
file with<collection-meta>
- bookiarcmono125.xml -- @lathrops1 please explain this sample in more detail. It's unclear to me why there are two collection-meta nodes. Is this for a wholebook in the PDF workflow?
@DioneMentis - This would be for any wholebook processed converted file.
There are two collection-meta nodes because each collection-type requires its own collection-meta wrapper.
This is collection information provided by a publisher about their Published Book Series (noted by the attribute book-series
)
<collection-meta collection-type="book-series">
<title-group>
<title>IARC Monographs on the Identification of Carcinogenic Hazards to Humans</title>
</title-group>
<volume-in-collection>
<volume-number>125</volume-number>
</volume-in-collection>
</collection-meta>
This is collection metadata that comes from the UI because it is NCBI-only collection information (note by the attribute 'ncbi-books-collection')
<collection-meta collection-type="ncbi-books-collection">
<collection-id collection-id-type="pmcid">iarcmonocollect</collection-id>
<title-group>
<title>IARC Monographs on the Identification of Carcinogenic Hazards to Humans</title>
</title-group>
</collection-meta>
Required from NCBI:
@DioneMentis I took real Bookshelf samples - we did not have any one with all fields.
-
complete samples for all fields in Column B (collection.xml) -
complete samples for all fields in Column E (writing node into chapter.cml files) -
complete samples for all fields in Column C (see examples and questions per section below)
Samples for collection-meta
and book-meta
follow; questions addressed below.
Metadata UI form and related XML output
PDF version of all updated UI tabs: collection-meta-UIs-20211110.pdf
Tab 1: Title and publisher information
- Title and IDs
<collection-id>domain name</collection-id>
<collection-name>NCBI collection title</collection-name>
ISSN
'type' is not required at this stage
@DioneMentis - if you are not pulling ISSN from converted XML here, we can keep to just one value and add types later.
<issn>0959-8138</issn>
- NCBI's custom meta 'Source type'
<custom-meta-wrap>
<custom-meta>
<meta-name>books-source-type</meta-name>
<meta-value>Collection</meta-value>
</custom-meta>
</custom-meta-wrap>
- Dropdown values for Wholebook and Chapter-processed:
- report
- book
- database
- documentation
- Publisher
<publisher>
<publisher-name>National Toxicology Program</publisher-name>
<publisher-loc>Research Triangle Park (NC)</publisher-loc>
</publisher>
- Publication date
Only print and electronic range is needed, where the end date is optional.
<pub-date pub-type="epubr">
<year>2012</year>
</pub-date>
- Abstract
Allow for multiple paragraphs.
<abstract>
<p>NTP Monographs contain literature-based evaluations of the evidence that environmental substances are associated with noncancer health effects or communicate the state of the science.</p>
</abstract>
Tab 2: Contributors
- Series editors and collaborative authors
<contrib-group>
<contrib contrib-type="editor">
<name>
<surname>Foster</surname>
<given-names>Bill</given-names>
</name>
<role>Series editor</role>
</contrib>
<contrib contrib-type="author">
<collab>National Academy of Sciences (US)</collab>
</contrib>
</contrib-group>
Tab 3: Permissions
Within the <permissions>
element, in order:
- Copyright statement:
Copyright year should be added in the statement. It is not required as a separate <copyright-year>
<copyright-statement>1997 Cold Spring Harbor Laboratory Press</copyright-statement>
- Licence information:
Below is what Denis is using to match CC license types in the UI to values in URLs. I don't know if this is sufficent for you to use. In his code he is missing the CC Public Domain value, which is the example you have in your markup and should be a drop down value. You can get all the URLs from this page by license type: https://creativecommons.org/about/cclicenses/
It matches the text in the url after the \licenses\ to the dropdown value
const ccMatch = ccLicense && ccLicense.match(/licenses/(.*?)//)
const ccLicenseType =
ccMatch && ccMatch.length === 2
? (matched => {
switch (matched) {
case 'by':
return 'CC BY'
case 'by-nc':
return 'CC BY-NC'
case 'by-nc-nd':
return 'CC BY-NC-ND'
case 'by-nc-sa':
return 'CC BY-NC-SA'
case 'by-nd':
return 'CC BY-ND'
case 'by-sa':
return 'CC BY-SA'
default:
return null
}
})(ccMatch[1])
: null
-
license-type
is "open access" when "Yes" is selected. when "No", thenlicense-type
orxlink:href
is not included. - Depending on type chosen, the relevant
xlink:href
is populated (information provided above)
<license license-type="open-access" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://creativecommons.org/publicdomain/zero/1.0/">
<license-p>This is a work of the US government and distributed under the terms of the Public Domain</license-p>
</license>
Tab 4: Notes
Note: currently there is a bug when selecting the note, type which makes the fields disappear.
- Type: disclaimer, author notes, generic, funder courtesy note
- Title is optional
- allow multiple paragraphs
- When funder courtesy note is selected, user has option to all to all PDF books in the collection
Disclamer
<notes notes-type="disclaimer">
<title>title</title>
<p>para</p>
</notes>
Author notes
<fn>
is required by the BITS DTD as a child of <author-notes>
to produce valid XML - see https://jats.nlm.nih.gov/extensions/bits/tag-library/2.0/element/author-notes.html. It does not need a label or necessary link / be related to anything, but is required as part of the markup.
<author-notes>
<fn><p>para</p></fn>
</author-notes>
Generic
<notes>
<p>para</p>
</notes>
Funder courtesy note
<notes notes-type=“courtesy-note”>
<p>Monographs, or book chapters, which are outputs of Wellcome Trust funding have been made freely available as part of the <ext-link xmlns:xlink=“http://www.w3.org/1999/xlink” ext-link-type=“uri” xlink:href=“https://wellcome.ac.uk/funding/guidance/open-access-policy”>Wellcome Trust’s open access policy</ext-link></p></notes>
Tab 5: Funding
See full Granthub spec in #433 (closed)
Acceptance criteria
See relevant sections in #776 (closed)