Feature request: Indicate papers that cite a Dandiset in the DLP
- Dominant language
- Python
- Stars
- 26
- Forks
- 21
- Avg merge
- 4d 23h
- Merged PRs (30d)
- 15
Description
I found a paper (https://doi.org/10.1016/j.neuron.2023.08.005) that cites Dandiset 000458 (https://doi.org/10.48324/dandi.000458/0.230317.0039). When I went to the Dandiset landing page, I find that there are some papers associated with this Dandiset but not the paper that I found. This is because the paper is a secondary use of this Dandiset, and did not exist when the Dandise was published.
I think we are missing a huge opportunity here. If we want to influence the behavior of scientists to reuse data, one of the best ways to do that is to educate them about others that are already doing this behavior. In doing so, we will establish that this is a high-quality dataset worth analyzing, demonstrate that you can achieve publications through reuse of data, and advance social norms around using data. All the better if the publications are from high-impact journals like Neuron. Therefore, I think in some way indicating papers that use and cite a Dandiset should be a high priority. While GitHub-like stars, page views, and download stats are all very important, IMO this metric is even more important than all of those.
I think this should really go on the DLP, and should _not_ be in control of the Dandiset owner. Ideally, this would reflect UX patterns that the user is already familiar with. For example every scientist is familiar with the Google Scholar "Cited By [x]" link:
I think the most straightforward UX solution would be to add a button here:
that says "Cited by [#]". Then that button would lead to a modal window that contains a list of papers that cite this Dandiset, formatted similarly to how this is done in Google Scholar:
This may not be ideal because it does not make the citation metrics as prominent as I would like, but it would be a massive improvement over not having this metric on the DLP at all.
Then the question is: how do we gather this information? It looks like this can be done with crossref (https://www.crossref.org/documentation/cited-by/retrieve-citations/), which would require credentials, and I don't know whether crossref even tracks using of DANDI DOIs.
opencitations provides a service for this that works on Science papers, e.g.
`http://opencitations.net/index/coci/api/v1/citations/10.1126/science.abf4588` but not on Dandisets.
`http://opencitations.net/index/coci/api/v1/citations/10.48324/dandi.000458/0.230317.0039` returns an empty list. It is possible the citations has just not been indexed yet. This is hard to test because a lot of publications like https://www.nature.com/articles/s41586-023-06031-6 do not properly cite the Dandiset DOI. This is another issue: we might want to be able to manually add citation information for examples like this where high-profile papers use Dandisets but do not cite them in a way that our system will be able to detect.
Once we have the DOIs of the citing papers, I can confirm that crossref is a great tool for gathering information about a specific publication. https://api.crossref.org/works/{doi} returns all the information we would need, e.g.
https://api.crossref.org/works/10.1126/science.abf4588
```python
{'DOI': '10.1126/science.abf4588',
'ISSN': ['0036-8075', '1095-9203'],
'URL': 'http://dx.doi.org/10.1126/science.abf4588',
'abstract': 'Recording many neurons for a long time\n'
' \n'
' The ultimate aim of chronic recordings is to sample '
'from the same neuron over days and weeks. However, this goal has '
'been difficult to achieve for large populations of neurons. '
'Steinmetz\n'
' et al.\n'
' describe the development and testing of Neuropixels '
'2.0. This new electrophysiological recording tool is a '
'miniaturized, high-density probe for both acute and long-term '
'experiments combined with sophisticated software algorithms for '
'fully automatic post hoc computational stabilization. The '
'technique also provides a strategy for extending the number of '
'recorded sites beyond the number of available recording '
'channels. In freely moving animals, extremely large numbers of '
'individual neurons could thus be followed and tracked with the '
'same probe for weeks and occasionally months.\n'
' \n'
' \n'
' Science\n'
' , this issue p.\n'
' eabf4588\n'
' ',
'alternative-id': ['10.1126/science.abf4588'],
'author': [{'ORCID': 'http://orcid.org/0000-0001-7029-2908',
'affiliation': [{'name': 'UCL Institute of Ophthalmology, '
'University College London, London, UK.'},
{'name': 'Department of Biological Structure, '
'University of Washington, Seattle, WA, '
'USA.'}],
'authenticated-orcid': True,
'family': 'Steinmetz',
'given': 'Nicholas A.',
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'container-title': ['Science'],
'content-domain': {'crossmark-restriction': False, 'domain': []},
'created': {'date-parts': [[2021, 4, 15]],
'date-time': '2021-04-15T19:51:33Z',
'timestamp': 1618516293000},
'deposited': {'date-parts': [[2024, 1, 15]],
'date-time': '2024-01-15T22:52:17Z',
'timestamp': 1705359137000},
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'doi-asserted-by': 'publisher',
'name': 'National Institutes of Health'},
{'DOI': '10.13039/100000875',
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{'DOI': '10.1016/j.neuron.2019.02.010',
'doi-asserted-by': 'publisher',
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{'DOI': '10.1038/s41593-019-0381-8',
'doi-asserted-by': 'publisher',
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{'DOI': '10.1101/772517',
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'unstructured': 'J. Park J. W. Phillips K. A. Martin A. W. '
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{'DOI': '10.1126/science.aao4960',
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{'DOI': '10.1038/s41593-019-0360-0',
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{'DOI': '10.7554/eLife.63035',
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{'DOI': '10.1016/j.neuron.2019.05.003',
'doi-asserted-by': 'publisher',
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{'DOI': '10.1073/pnas.1717695114',
'doi-asserted-by': 'publisher',
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{'DOI': '10.1016/j.neuron.2018.11.002',
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{'DOI': '10.2196/16194',
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{'DOI': '10.1088/1741-2560/10/4/046016',
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{'DOI': '10.1126/sciadv.1601966',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_33_2'},
{'DOI': '10.1152/jn.00352.2020',
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'key': 'e_1_3_2_34_2'},
{'DOI': '10.1088/1741-2552/ab8343',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_35_2'},
{'article-title': 'The tetrode: A new technique for multi-unit '
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'author': 'Recce M.',
'first-page': '1250',
'journal-title': 'Soc. Neurosci. Abstr.',
'key': 'e_1_3_2_36_2',
'unstructured': 'M. Recce, J. O’Keefe, The tetrode: A new '
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'recording. Soc. Neurosci. Abstr. 15, 1250 '
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'volume': '15',
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{'DOI': '10.7554/eLife.27702',
'doi-asserted-by': 'publisher',
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{'DOI': '10.1016/S0013-4694(96)95176-0',
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{'DOI': '10.1088/1741-2560/8/4/045005',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_39_2'},
{'DOI': '10.1371/journal.pone.0151180',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_40_2'},
{'DOI': '10.1101/2020.08.09.243279',
'doi-asserted-by': 'crossref',
'key': 'e_1_3_2_41_2',
'unstructured': 'J.-O. Muthmann A. J. Levi H. C. Carney A. C. '
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'system for electrophysiology spanning '
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{'DOI': '10.1101/2020.09.24.312132',
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'key': 'e_1_3_2_42_2',
'unstructured': 'C. E. Schoonover S. N. Ohashi R. Axel A. J. '
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'olfactory cortex. bioRxiv 2020.09.24.312132 '
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'https://doi.org/10.1101/2020.09.24.312132.'},
{'DOI': '10.7554/eLife.47188',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_43_2'},
{'DOI': '10.1016/j.jneumeth.2003.12.022',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_44_2'},
{'DOI': '10.1152/jn.00569.2007',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_45_2'},
{'DOI': '10.1152/jn.00260.2007',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_46_2'},
{'DOI': '10.1152/jn.90920.2008',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_47_2'},
{'DOI': '10.1152/jn.01012.2010',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_48_2'},
{'DOI': '10.1152/jn.00052.2014',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_49_2'},
{'DOI': '10.1152/jn.00464.2015',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_50_2'},
{'DOI': '10.1021/acs.nanolett.6b02673',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_51_2'},
{'DOI': '10.1109/TBME.2015.2406113',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_52_2'},
{'DOI': '10.1101/742346',
'doi-asserted-by': 'crossref',
'key': 'e_1_3_2_53_2',
'unstructured': 'M. S. Saleh S. M. Ritchie M. A. Nicholas R. '
'Bezbaruah J. W. Reddy M. Chamanzar E. A. '
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{'DOI': '10.1126/sciadv.aay2789',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_54_2'},
{'DOI': '10.1088/1741-2552/abd0ce',
'article-title': 'The Argo: A high channel count recording '
'system for neural recording in vivo',
'author': 'Sahasrabuddhe K.',
'doi-asserted-by': 'crossref',
'journal-title': 'J. Neural Eng.',
'key': 'e_1_3_2_55_2',
'unstructured': 'K. Sahasrabuddhe, A. A. Khan, A. P. Singh, T. '
'M. Stern, Y. Ng, A. Tadić, P. Orel, C. '
'LaReau, D. Pouzzner, K. Nishimura, K. M. '
'Boergens, S. Shivakumar, M. S. Hopper, B. '
'Kerr, M. S. Hanna, R. J. Edgington, I. '
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'S. Veijalainen, A. V. Klekachev, A. M. '
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'high channel count recording system for '
'neural recording in vivo. J. Neural Eng. 18, '
'015002 (2021). 33624614',
'volume': '18',
'year': '2021'},
{'DOI': '10.1038/nature03274',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_56_2'},
{'DOI': '10.1152/jn.00747.2006',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_57_2'},
{'DOI': '10.1523/JNEUROSCI.2974-11.2011',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_58_2'},
{'DOI': '10.3389/fncir.2011.00018',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_59_2'},
{'DOI': '10.1523/JNEUROSCI.4071-12.2013',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_60_2'},
{'DOI': '10.1371/journal.pone.0008222',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_61_2'},
{'DOI': '10.1101/2020.10.05.327049',
'doi-asserted-by': 'crossref',
'key': 'e_1_3_2_62_2',
'unstructured': 'D. Deitch A. Rubin Y. Ziv Representational '
'drift in the mouse visual cortex. bioRxiv '
'2020.10.05.327049 [Preprint]. 5 October 2020. '
'https://doi.org/10.1101/2020.10.05.327049.'},
{'DOI': '10.1101/2020.12.10.420620',
'doi-asserted-by': 'crossref',
'key': 'e_1_3_2_63_2',
'unstructured': 'T. D. Marks M. J. Goard Stimulus-dependent '
'representational drift in primary visual '
'cortex. bioRxiv 2020.12.10.420620 [Preprint]. '
'11 December 2020. '
'https://doi.org/10.1101/2020.12.10.420620.'},
{'DOI': '10.1101/851691',
'doi-asserted-by': 'crossref',
'key': 'e_1_3_2_64_2',
'unstructured': 'K. H. Lee Y.-L. Ni M. Meister Electrode '
'pooling: How to boost the yield of switchable '
'silicon probes for neuronal recordings. '
'bioRxiv 851691 [Preprint]. 26 November 2019. '
'https://doi.org/10.1101/851691.'},
{'DOI': '10.1152/jn.00979.2005',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_65_2'},
{'DOI': '10.1016/j.jneumeth.2018.08.020',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_66_2'},
{'DOI': '10.1109/TBCAS.2019.2942450',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_67_2'},
{'DOI': '10.1109/TBCAS.2019.2943077',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_68_2'},
{'key': 'e_1_3_2_69_2',
'unstructured': 'N. Steinmetz M. Okun Ç. Aydın Code and '
'summary data for Steinmetz et al. '
'“Neuropixels 2.0: A miniaturized high-density '
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'“Neuropixels 2.0: A miniaturized high-density '
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{'key': 'e_1_3_2_71_2',
'unstructured': 'M. Pachitariu C. Rossant N. Steinmetz J. '
'Colonell A. G. Bondy O. Winter K. Banga J. '
'Bhagat M. Sosa D. O’Shea J. Guzman K. C. '
'Nakamura Geffen Lab P. Botros R. Saxena A. '
'Liddell J. Pellman M. Spacek D. Bryzgalov C. '
'Stringer D. Denman D. Karamanlis M. Beau '
'Kilosort 2.5 Software package for Steinmetz '
'et al. “Neuropixels 2.0: A miniaturized '
'high-density probe for stable long-term brain '
'recordings.” Version 2.5 Zenodo (2021); '
'https://doi.org/10.5281/zenodo.4482749.'},
{'key': 'e_1_3_2_72_2',
'unstructured': 'Ç. Aydin R. van Daal CAD files for Steinmetz '
'et al. “Neuropixels 2.0: A miniaturized '
'high-density probe for stable long-term brain '
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{'DOI': '10.1371/journal.pone.0089007',
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{'DOI': '10.1016/j.cell.2015.08.014',
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{'DOI': '10.1038/nn.3078',
'doi-asserted-by': 'publisher',
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{'article-title': 'A statistical approach to some basic mine '
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'journal-title': 'J. South. Afr. Inst. Min. Metall.',
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'unstructured': 'D. G. Krige, A statistical approach to some '
'basic mine valuation problems on the '
'Witwatersrand. J. South. Afr. Inst. Min. '
'Metall. 52, 119–139 (1951).',
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'year': '1951'},
{'DOI': '10.1371/journal.pone.0062123',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_77_2'},
{'DOI': '10.1101/061481',
'doi-asserted-by': 'crossref',
'key': 'e_1_3_2_78_2',
'unstructured': 'M. Pachitariu N. Steinmetz S. Kadir M. '
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'electrophysiology with hundreds of channels. '
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{'DOI': '10.1109/83.988953',
'doi-asserted-by': 'publisher',
'key': 'e_1_3_2_79_2'},
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'unstructured': 'M. Pachitariu C. Stringer M. Dipoppa S. '
'Schröder L. F. Rossi H. Dalgleish M. '
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'neurons with standard two-photon microscopy. '
'bioRxiv 061507 [Preprint]. 20 July 2017. '
'https://doi.org/10.1101/061507.10.1101/061507'},
{'DOI': '10.1038/nn.4268',
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'Implantation of Neuropixels probes for '
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'freely behaving mice and rats. Nat. Protoc. '
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```
Beyond putting on the DLP, this is a very important metric for us to track. Looking at publications over the last year or so, I am seeing examples of high-profile papers that use Dandisets that we don't even know about, and this is quickly getting to a point where we need automated tools to track this.
1. What is the best way to automatically track this information?
2. How does the team feel about displaying this information on the DLP?
Contributor guide
No contributing guide indexed for this repository
Research direction
Start with the DLP Dandiset landing page and review how its existing associated-paper information is presented. Investigate Crossref's cited-by retrieval and the provided OpenCitations examples, including handling papers that do not cite Dandiset DOIs cleanly. Done should define a viable source of citation data and present a cited-by count with a paper list in the landing-page UX.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- django, python
- Domain
- backend-api-design, full-stack
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 30/100