Closed clairerye closed 3 years ago
clairerye
commented
3 years ago @mshadbolt and @jacobwindsor when you get the chance are you able to add details here of the current script and if you had thoughts on automating it... I think we had at one point discussed adding an end point specifically for this in ingest core?
mshadbolt
commented
3 years ago What kind of details are you after here? The details about the script and how it is run is in the readme of the repo https://github.com/ebi-ait/projects-index. Are there specific details we are missing that you want outlined?
My understanding on automating it is that it would require some way of flagging on a project in ingest when it should be included in the catalogue and then setting up an API endpoint that you could query for those projects.
@jacobwindsor would be able to speak more about the technicalities of that.
In addition, it would be good to automate the project level organs and technologies as I don't think these are routinely filled in but should be able to be automated by periodically querying the submission metadata and storing against the project. You wouldn't want to do this 'on the fly' as it can be very slow if there are a lot of metadata entities.
Another blocker for the automation of this is that wranglers still tend to leave multiple copies of the same project in ingest during testing. I have tried multiple times to follow up and request one project be left in Prod but I have given up after multiple requests and not much traction. Maybe we could enforce something in ingest which doesn't allow two projects with the same title/shortname the same way we don't allow the doi to be duplicated when using that feature?
clairerye
commented
3 years ago Thanks @mshadbolt this is exactly what I was after.
jacobwindsor
commented
3 years ago Thanks for the summary @mshadbolt.
For flagging a project in ingest, we could just add a property (which would require some db migration). For querying, I see two options. A new endpoint (e.g. /projects/published) or we set up Solr and we can use that to query only projects with the published facet. We could then use Solr in other places in ingest. Obviously, the latter is a bigger time cost but will have future advantages (e.g. BioSolr ontology searching in ingest and project catalogue) (@clairerye?)
clairerye
commented
3 years ago So it sounds like we need the "published" facet either way, maybe that is a first step? I really like the idea of being able to do ontology searching in ingest and project catalogue. Being able to query our super rich metadata is one of the key points of collecting it so +1 to this idea from me.
jacobwindsor
commented
3 years ago @clairerye Yes, either way we will need the published property so that is a good start.
Solr will obviously take some more time but I can have a chat with Isuru and Amnon to get an estimate on this. I'm not really sure myself
clairerye
commented
3 years ago Remove the script, and create an API end point to query directly
MightyAx
commented
3 years ago Also possibly add wrangling status
clairerye
commented
3 years ago Absolutely - but I think we should call this out of scope for now
jacobwindsor
commented
3 years ago Draft PR for core: https://github.com/ebi-ait/ingest-core/pull/65 Gist for script to update previously published projects: https://gist.github.com/jacobwindsor/095f7d59bf755207cc547e9d9a154e51
MightyAx
commented
3 years ago We can now also set the publications for these 12 projects manually, even though the projects "in ingest" have no publication info:
These 3 have no Project MetaData:
These 9 have no publication info:
MightyAx
commented
3 years ago Project UUIDs that were in the old version of the catalogue that do not exist in ingest:
MightyAx
commented
3 years ago For Review by @gabsie
gabsie
commented
3 years ago Hi, @MightyAx
I would propose this text, so that a submitter is not confused by the word Publish
Include this project in the Human Cell Atlas Project Catalogue by EMBL-EBI
(Description: Your project will appear with its name, authors, publication, and data accession links when available.)
@clairerye?
Gabs
clairerye
commented
3 years ago sounds good to me
MightyAx
commented
3 years ago @gabsie
Description: Your project will appear with its name, authors, publication, and data accession links when available.
To confirm, should the guide text should be A or B? If B, we will have not link to the Human Cell Atlas Project Catalogue by EMBL-EBI and the user will have to google it.
The Human Cell Atlas Project Catalogue by EMBL-EBI aims to provide a comprehensive list of all the cellular resolution data generated by and available to the HCA community. Your project will appear with its name, authors, publication, and data accession links when available.
Your project will appear with its name, authors, publication, and data accession links when available.
gabsie
commented
3 years ago Good thought, Alexie. Especially as I want to make all these guide texts in tooltips in the future , because they take up too much space. I shortened it by a few words.
The Human Cell Atlas Project Catalogue by EMBL-EBI provides a comprehensive list of all the cellular resolution data available to the HCA community. Your project will appear with its name, authors, publication, and data accession links when available.
MightyAx
commented
3 years ago Catalogue script run on production:
Updating project 027c51c6-0719-469f-a7f5-640fe57cbece: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1681/ASN.2018020125', 'url': 'http://dx.doi.org/10.1681/asn.2018020125', 'journalTitle': 'Journal of the American Society of Nephrology', 'title': 'Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response', 'authors': ['Wu H', 'Malone AF', 'Donnelly EL', 'Kirita Y', 'Uchimura K', 'Ramakrishnan SM', 'Gaut JP', 'Humphreys BD']}]}
Updating project 0b2cbf1a-3f40-4e01-a99d-901fa6091ee5: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.devcel.2020.11.010', 'url': 'http://dx.doi.org/10.1016/j.devcel.2020.11.010', 'journalTitle': 'Developmental Cell', 'title': 'Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease', 'authors': ['Elmentaite R', 'Ross, A', 'James KR', 'Ortmann D', 'Gomes T', 'Roberts K', 'Nayak K', 'Tuck L', 'Bayraktar OA', 'Heuschkel R', 'Vallier L', 'Teichmann SA', 'Zilbauer M']}]}
Updating project 116965f3-f094-4769-9d28-ae675c1b569c: {'isInCatalogue': True}
Updating project 1cd1f41f-f81a-486b-a05b-66ec60f81dcf: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1126/sciadv.aau4788', 'url': 'http://dx.doi.org/10.1126/sciadv.aau4788', 'journalTitle': 'Science Advances', 'title': 'A single-cell survey of the human first-trimester placenta and decidua', 'authors': ['Suryawanshi H', 'Morozov P', 'Straus A', 'Sahasrabudhe N', 'Max KEA', 'Garzia A', 'Kustagi M', 'Tuschl T', 'Williams Z']}]}
Updating project 1defdada-a365-44ad-9b29-443b06bd11d6: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-019-0933-9', 'url': 'http://dx.doi.org/10.1038/s41586-019-0933-9', 'journalTitle': 'Nature', 'title': 'A single-cell molecular map of mouse gastrulation and early organogenesis', 'authors': ['Pijuan-Sala B', 'Griffiths JA', 'Guibentif C', 'Hiscock TW', 'Jawaid W', 'Calero-Nieto FJ', 'Mulas C', 'Ibarra-Soria X', 'Tyser RCV', 'Ho DLL', 'Reik W', 'Srinivas S', 'Simons BD', 'Nichols J', 'Marioni JC', 'Göttgens B']}]}
Updating project 2043c65a-1cf8-4828-a656-9e247d4e64f1: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.neuron.2017.02.014', 'url': 'http://dx.doi.org/10.1016/j.neuron.2017.02.014', 'journalTitle': 'Neuron', 'title': 'Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.', 'authors': ['Close JL', 'Yao Z', 'Levi BP', 'Miller JA', 'Bakken TE', 'Menon V', 'Ting JT', 'Wall A', 'Krostag AR', 'Thomsen ER', 'Nelson AM', 'Mich JK', 'Hodge RD', 'Shehata SI', 'Glass IA', 'Bort S', 'Shapovalova NV', 'Ngo NK', 'Grimley JS', 'Phillips JW', 'Thompson CL', 'Ramanathan S', 'Lein E']}]}
Updating project 2086eb05-10b9-432b-b7f0-169ccc49d270: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1161/CIRCRESAHA.118.314578', 'url': 'http://dx.doi.org/10.1161/circresaha.118.314578', 'journalTitle': 'Circulation Research', 'title': 'Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution.', 'authors': ['Goodyer WR', 'Beyersdorf BM', 'Paik DT', 'Tian L', 'Buikema JW', 'Chirikian O', 'Choi S', 'Venkatraman S', 'Adams EL', 'Tessier-Lavigne M', 'Wu JC', 'Wu SM']}]}
Updating project 2ef3655a-973d-4d69-9b41-21fa4041eed7: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41597-019-0351-8', 'url': 'http://dx.doi.org/10.1038/s41597-019-0351-8', 'journalTitle': 'Scientific Data', 'title': 'Single-cell RNA sequencing of human kidney', 'authors': ['Liao J', 'Yu Z', 'Chen Y', 'Bao M', 'Zou C', 'Zhang H', 'Liu D', 'Li T', 'Zhang Q', 'Li J', 'Cheng J', 'Mo Z']}]}
Updating project 3089d311-f9ed-44dd-bb10-397059bad4dc: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.immuni.2019.11.014', 'url': 'http://dx.doi.org/10.1016/j.immuni.2019.11.014', 'journalTitle': 'Immunity', 'title': 'Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer.', 'authors': ['Cillo AR', 'Kürten CHL', 'Tabib T', 'Qi Z', 'Onkar S', 'Wang T', 'Liu A', 'Duvvuri U', 'Kim S', 'Soose RJ', 'Oesterreich S', 'Chen W', 'Lafyatis R', 'Bruno TC', 'Ferris RL', 'Vignali DAA']}]}
Updating project 3138bf07-b24a-49c8-b1f3-61329d7abc3b: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s42003-020-0922-4', 'url': 'http://dx.doi.org/10.1038/s42003-020-0922-4', 'journalTitle': 'Communications Biology', 'title': 'Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming.', 'authors': ['Solé-Boldo L', 'Raddatz G', 'Schütz S', 'Mallm JP', 'Rippe K', 'Lonsdorf AS', 'Rodríguez-Paredes M', 'Lyko F']}]}
Updating project 38449aea-70b5-40db-84b3-1e08f32efe34: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-019-0903-2', 'url': 'http://dx.doi.org/10.1038/s41586-019-0903-2', 'journalTitle': 'Nature', 'title': 'Altered human oligodendrocyte heterogeneity in multiple sclerosis', 'authors': ['Jäkel S', 'Agirre E', 'Falcão AM', 'van Bruggen D', 'Lee KW', 'Knuesel I', 'Malhotra D', 'ffrench-Constant C', 'Williams A', 'Castelo-Branco G']}]}
Updating project 42d4f8d4-5422-4b78-adae-e7c3c2ef511c: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1126/science.aav2501', 'url': 'http://dx.doi.org/10.1126/science.aav2501', 'journalTitle': 'Science', 'title': 'Identification of a mesenchymal progenitor cell hierarchy in adipose tissue.', 'authors': ['Merrick D', 'Sakers A', 'Irgebay Z', 'Okada C', 'Calvert C', 'Morley MP', 'Percec I', 'Seale P']}]}
Updating project 453d7ee2-319f-496c-9862-99d397870b63: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41591-018-0096-5', 'url': 'http://dx.doi.org/10.1038/s41591-018-0096-5', 'journalTitle': 'Nature Medicine', 'title': 'Phenotype molding of stromal cells in the lung tumor microenvironment', 'authors': ['Lambrechts D, Wauters E, Boeckx B, Aibar S, Nittner D, Burton O, Bassez A, Decaluwé H, Pircher A, Van den Eynde K, Weynand B, Verbeken E, De Leyn P, Liston A, Vansteenkiste J, Carmeliet P, Aerts S, Thienpont B']}]}
Updating project 4a95101c-9ffc-4f30-a809-f04518a23803: {'isInCatalogue': True}
Updating project 4d6f6c96-2a83-43d8-8fe1-0f53bffd4674: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41467-018-06318-7', 'url': 'http://dx.doi.org/10.1038/s41467-018-06318-7', 'journalTitle': 'Nature Communications', 'title': 'Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations', 'authors': ['MacParland SA', 'Liu JC', 'Ma XZ', 'Innes BT', 'Bartczak AM', 'Gage BK', 'Manuel J', 'Khuu N', 'Echeverri J', 'Linares I', 'Gupta R', 'Cheng ML', 'Liu LY', 'Camat D', 'Chung SW', 'Seliga RK', 'Shao Z', 'Lee E', 'Ogawa S', 'Ogawa M', 'Wilson MD', 'Fish JE', 'Selzner M', 'Ghanekar A', 'Grant D', 'Greig P', 'Sapisochin G', 'Selzner N', 'Winegarden N', 'Adeyi O', 'Keller G', 'Bader GD', 'McGilvray ID']}]}
Updating project 4e6f083b-5b9a-4393-9890-2a83da8188f1: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-019-1127-1', 'url': 'http://dx.doi.org/10.1038/s41586-019-1127-1', 'journalTitle': 'Nature', 'title': 'The emergent landscape of the mouse gut endoderm at single-cell resolution', 'authors': ["Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Vincent Liu, Vidur Garg, Roshan Sharma, Claire S. Simon, Nestor Saiz, Rui Gardner, Stéphane C. Boutet, Deanna M. Church, Pamela A. Hoodless, Anna-Katerina Hadjantonakis, Dana Pe'er"]}]}
Updating project 559bb888-7829-41f2-ace5-2c05c7eb81e9: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41421-020-0157-z', 'url': 'http://dx.doi.org/10.1038/s41421-020-0157-z', 'journalTitle': 'Cell Discovery', 'title': 'Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human.', 'authors': ['Zhao J', 'Zhang S', 'Liu Y', 'He X', 'Qu M', 'Xu G', 'Wang H', 'Huang M', 'Pan J', 'Liu Z', 'Li Z', 'Liu L', 'Zhang Z']}]}
Updating project 577c946d-6de5-4b55-a854-cd3fde40bff2: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/645424', 'url': 'http://dx.doi.org/10.1101/645424', 'journalTitle': 'bioRxiv', 'title': 'The Single Cell Transcriptomic Landscape of Early Human Diabetic Nephropathy', 'authors': ['Humphreys BD', 'Wilson PC', 'Rennke HG', 'Welling PA', 'Waikar SS', 'Wu H', 'Kirita Y', 'Uchimura K']}]}
Updating project 5b5f05b7-2482-468d-b76d-8f68c04a7a47: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/459891', 'url': 'http://dx.doi.org/10.1101/459891', 'journalTitle': 'bioRxiv', 'title': 'Single-cell multi-omic integration compares and contrasts features of brain cell identity', 'authors': ['Welch J', 'Kozareva V', 'Ferreira A', 'Vanderburg C', 'Martin C', 'Macosko E']}]}
Updating project 6c040a93-8cf8-4fd5-98de-2297eb07e9f6: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-019-1917-5', 'url': 'http://dx.doi.org/10.1038/s41586-019-1917-5', 'journalTitle': 'Nature', 'title': 'Decoding the development of the human hippocampus.', 'authors': ['Zhong S', 'Ding W', 'Sun L', 'Lu Y', 'Dong H', 'Fan X', 'Liu Z', 'Chen R', 'Zhang S', 'Ma Q', 'Tang F', 'Wu Q', 'Wang X']}]}
Updating project 7027adc6-c9c9-46f3-84ee-9badc3a4f53b: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1242/dev.180398', 'url': 'http://dx.doi.org/10.1242/dev.180398', 'journalTitle': 'Development', 'title': 'A cellular atlas of Pit2x-dependent cardiac development.', 'authors': ['Hill MC', 'Kadow ZA', 'Li L', 'Tran TT', 'Wythe JD', 'Martin JF']}]}
Updating project 74b6d569-3b11-42ef-b6b1-a0454522b4a0: {'isInCatalogue': True}
Updating project 8185730f-4113-40d3-9cc3-929271784c2b: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.15252/embj.2018100811', 'url': 'http://dx.doi.org/10.15252/embj.2018100811', 'journalTitle': 'The EMBO Journal', 'title': 'A single‐cell transcriptome atlas of the adult human retina', 'authors': ['Lukowski SW', 'Lo CY', 'Sharov AA', 'Nguyen Q', 'Fang L', 'Hung SS', 'Zhu L', 'Zhang T', 'Grünert U', 'Nguyen T', 'Senabouth A', 'Jabbari JS', 'Welby E', 'Sowden JC', 'Waugh HS', 'Mackey A', 'Pollock G', 'Lamb TD', 'Wang PY', 'Hewitt AW', 'Gillies MC', 'Powell JE', 'Wong RC']}]}
Updating project 83f5188e-3bf7-4956-9544-cea4f8997756: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2019.12.12.871657', 'url': 'http://dx.doi.org/10.1101/2019.12.12.871657', 'journalTitle': 'bioRxiv', 'title': 'Distinct microbial and immune niches of the human colon', 'authors': ['Meyer KB', 'Elmentaite R', 'Gomes T', 'Petrova VN', 'Kumar N', 'Polanski K', 'Lawley TD', 'Stares MD', 'Gulliver EL', 'Clatworthy MR', 'Ferdinand JR', 'Bareham BR', 'Forster SC', 'Howlett S', 'Jarvis LB', 'King HW', 'Saeb-Parsy K', 'Suchanek O', 'James LK', 'Jones JL', 'Teichmann SA']}, {'doi': '10.1038/s41590-020-0602-z', 'url': 'http://dx.doi.org/10.1038/s41590-020-0602-z', 'journalTitle': 'Nature Immunology', 'title': 'Distinct microbial and immune niches of the human colon', 'authors': ['Meyer KB', 'Elmentaite R', 'Gomes T', 'Petrova VN', 'Kumar N', 'Polanski K', 'Lawley TD', 'Stares MD', 'Gulliver EL', 'Clatworthy MR', 'Ferdinand JR', 'Bareham BR', 'Forster SC', 'Howlett S', 'Jarvis LB', 'King HW', 'Saeb-Parsy K', 'Suchanek O', 'James LK', 'Jones JL', 'Teichmann SA']}]}
Updating project 87215108-e533-4364-abd4-0fe71edd35c1: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1681/ASN.2018020125', 'url': 'http://dx.doi.org/10.1681/asn.2018020125', 'journalTitle': 'Journal of the American Society of Nephrology', 'title': 'Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response', 'authors': ['Wu H', 'Malone AF', 'Donnelly EL', 'Kirita Y', 'Uchimura K', 'Ramakrishnan SM', 'Gaut JP', 'Humphreys BD']}]}
Updating project 88ec040b-8705-4f77-8f41-f81e57632f7d: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/632216', 'url': 'http://dx.doi.org/10.1101/632216', 'journalTitle': 'bioRxiv', 'title': 'Systematic comparative analysis of single cell RNA-sequencing methods', 'authors': ['Ding J;Adiconis X;Simmons SK;Kowalczyk MS;Hession CC;Marjanovic ND;Hughes TK;MH Wadsworth MH;Burks T;Nguyen LT;Kwon JY;Barak B;Ge W;Kedaigle AJ;Carroll S;Li S;Hacohen N;Rozenblatt-Rosen O;Shalek AK;Villani C;Regev A;Levin JZ']}]}
Updating project 8c3c290d-dfff-4553-8868-54ce45f4ba7f: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/467225', 'url': 'http://dx.doi.org/10.1101/467225', 'journalTitle': 'bioRxiv', 'title': 'Single-cell RNA sequencing reveals a dynamic stromal niche within the evolving tumour microenvironment', 'authors': ['Davidson S', 'Efremova M', 'Riedel A', 'Mahata B', 'Pramanik J', 'Huuhtanen F', 'Kar G', 'Vento-Tormo R', 'Hagai T', 'Chen X', 'Haniffa MA', 'Shields JD', 'Teichmann SA']}]}
Updating project 90bd6933-40c0-48d4-8d76-778c103bf545: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1126/sciimmunol.aan8664', 'url': 'http://dx.doi.org/10.1126/sciimmunol.aan8664', 'journalTitle': 'Science Immunology', 'title': 'Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis.', 'authors': ['Patil VS', 'Madrigal A', 'Schmiedel BJ', 'Clarke J', 'ORourke P', 'Harris E', 'de Silva AD', 'Harris E', 'Peters B', 'Seumois G', 'Weiskopf D', 'Sette A', 'Vijayanand P']}]}
Updating project 95f07e6e-6a73-4e1b-a880-c83996b3aa5c: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1126/sciimmunol.abd1554', 'url': 'http://dx.doi.org/10.1126/sciimmunol.abd1554', 'journalTitle': 'Science Immunology', 'title': 'Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19.', 'authors': ['Lee JS', 'Park S', 'Jeong HW', 'Ahn JY', 'Choi SJ', 'Lee H', 'Choi B', 'Nam SK', 'Sa M', 'Kwon JS', 'Jeong SJ', 'Lee HK', 'Park SH', 'Park SH', 'Choi JY', 'Kim SH', 'Jung I', 'Shin EC']}]}
Updating project 996120f9-e84f-409f-a01e-732ab58ca8b9: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41467-020-17876-0', 'url': 'http://dx.doi.org/10.1038/s41467-020-17876-0', 'journalTitle': 'Nature Communications', 'title': 'A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders.', 'authors': ['Agarwal D', 'Sandor C', 'Volpato V', 'Caffrey TM', 'Monzón-Sandoval J', 'Bowden R', 'Alegre-Abarrategui J', 'Wade-Martins R', 'Webber C']}]}
Updating project a29952d9-925e-40f4-8a1c-274f118f1f51: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41591-018-0269-2', 'url': 'http://dx.doi.org/10.1038/s41591-018-0269-2', 'journalTitle': 'Nature Medicine', 'title': 'Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma', 'authors': ['Ledergor, G', 'Weiner, A', 'Zada, M', 'Wang, S-Y', 'Cohen, YC', 'Gatt, ME', 'Snir, N', 'Magen, H', 'Koren-Michowitz, M', 'Herzog-Tzarfati, K', 'Keren-Shaul, H', 'Bornstein, C', 'Rotkopf, R', 'Yofe, I', 'David, E', 'Yellapantula, V', 'Kay, S', 'Salai, M', 'Ben Yehuda, D', 'Nagler, A', 'Shvidel, L', 'Orr-Urtreger, A', 'Halpern, KB', 'Itzkovitz, S', 'Landgren, O', 'San-Miguel, J', 'Paiva, B', 'Keats, JJ', 'Papaemmanuil, E', 'Avivi, I', 'Barbash, GI', 'Tanay, A', 'Amit, I']}]}
Updating project a72bed96-a4f7-401a-a67a-17b8a7357faf: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.7554/eLife.36865', 'url': 'http://dx.doi.org/10.7554/elife.36865', 'journalTitle': 'eLife', 'title': 'Pdgfra marks a cellular lineage with distinct contributions to myofibroblasts in lung maturation and injury response.', 'authors': ['Li R', 'Bernau K', 'Sandbo N', 'Gu J', 'Preissl S', 'Sun X', '']}]}
Updating project a815c84b-8999-433f-958e-422c0720e00d: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/nature25980', 'url': 'http://dx.doi.org/10.1038/nature25980', 'journalTitle': 'Nature', 'title': 'A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.', 'authors': ['Zhong S', 'Zhang S', 'Fan X', 'Wu Q', 'Yan L', 'Dong J', 'Zhang H', 'Li L', 'Sun L', 'Pan N', 'Xu X', 'Tang F', 'Zhang J', 'Qiao J', 'Wang X']}]}
Updating project a9c022b4-c771-4468-b769-cabcf9738de3: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/585901', 'url': 'http://dx.doi.org/10.1101/585901', 'journalTitle': 'bioRxiv', 'title': 'Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation', 'authors': ['Selewa Alan', 'Dohn Ryan', 'Eckart Heather', 'Lozano Stephanie', 'Xie Bingqing', 'Gauchat Eric', 'Elorbany Reem', 'Rhodes Katherine', 'Burnett Jonathan', 'Gilad Yoav', 'Pott Sebastian', 'Basu Anindita']}]}
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Updating project e579d0f4-18ef-4d42-90fa-4d2afb60a862: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.stem.2019.12.005', 'url': 'http://dx.doi.org/10.1016/j.stem.2019.12.005', 'journalTitle': 'Cell Stem Cell', 'title': 'The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty.', 'authors': ['Guo J', 'Nie X', 'Giebler M', 'Mlcochova H', 'Wang Y', 'Grow EJ', '', 'Kim R', 'Tharmalingam M', 'Matilionyte G', 'Lindskog C', 'Carrell DT', 'Mitchell RT', 'Goriely A', 'Hotaling JM', 'Cairns BR']}]}
Updating project f2fe82f0-4454-4d84-b416-a885f3121e59: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-019-1652-y', 'url': 'http://dx.doi.org/10.1038/s41586-019-1652-y', 'journalTitle': 'Nature', 'title': 'Decoding human fetal liver haematopoiesis', 'authors': ['Popescu D-M', 'Botting RA', 'Stephenson E', 'Green K', 'Jardine L', 'Calderbank EF', 'Efremova M', 'Acres M', 'Maunder D', 'Vegh P', 'Goh I', 'Gitton Y', 'Park J', 'Polanski K', 'Vento-Tormo R', 'Miao Z', 'Rowell R', 'McDonald D', 'Fletcher J', 'Dixon D', 'Poyner E', 'Reynolds G', 'Mather M', 'Moldovan C', 'Mamanova L', 'Greig F', 'Young M', 'Meyer K', 'Lisgo S', 'Bacardit J', 'Fuller A', 'Millar B', 'Innes B', 'Lindsay S', 'Stubbington MJT', 'Kowalczyk MS', 'Li B', 'Ashenbrg O', 'Tabaka M', 'Dionne D', 'Tickle TL', 'Slyper M', 'Rozenblatt-Rosen O', 'Filby A', 'Villani A-C', 'Roy A', 'Regev A', 'Chedotal A', 'Roberts I', 'Göttgens B', 'Laurenti E', 'Behjati S', 'Teichmann SA', 'Haniffa M']}]}
Updating project f48e7c39-cc67-4055-9d79-bc437892840c: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.3389/fcell.2020.00384', 'url': 'http://dx.doi.org/10.3389/fcell.2020.00384', 'journalTitle': 'Frontiers in Cell and Developmental Biology', 'title': 'Single-Cell RNA-Seq Analysis Uncovers Distinct Functional Human NKT Cell Sub-Populations in Peripheral Blood.', 'authors': ['Zhou L', 'Adrianto I', 'Wang J', 'Wu X', 'Datta I', 'Mi QS']}]}
Updating project f81efc03-9f56-4354-aabb-6ce819c3d414: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1186/s13059-018-1603-1', 'url': 'http://dx.doi.org/10.1186/s13059-018-1603-1', 'journalTitle': 'Genome Biology', 'title': 'Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics', 'authors': ['Stoeckius M', 'Zheng S', 'Houck-Loomis B', 'Hao S', 'Yeung BZ', 'Mauck III WM', 'Smibert P', 'Satija R']}]}
Updating project f83165c5-e2ea-4d15-a5cf-33f3550bffde: {'isInCatalogue': True}
Updating project f86f1ab4-1fbb-4510-ae35-3ffd752d4dfc: {'isInCatalogue': True}
Updating project f8aa201c-4ff1-45a4-890e-840d63459ca2: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.cell.2018.08.067', 'url': 'http://dx.doi.org/10.1016/j.cell.2018.08.067', 'journalTitle': 'Cell', 'title': 'Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease', 'authors': ['Kinchen J', 'Chen HH', 'Parikh K', 'Antanaviciute A', 'Jagielowicz M', 'Fawkner-Corbett D', 'Ashley N', 'Cubitt L', 'Mellado-Gomez E', 'Attar M', 'Sharma E', 'Wills Q', 'Bowden R', 'Richter FC', 'Ahern D', 'Puri KD', 'Henault J', 'Gervais F', 'Koohy H', 'Simmons A']}]}
Updating project fc232d87-7b10-47f7-9197-b2c6cf210dea: {'isInCatalogue': True}
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Updating project 6936da41-3692-46bb-bca1-cd0f507991e9: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-020-2922-4', 'url': 'http://dx.doi.org/10.1038/s41586-020-2922-4', 'journalTitle': 'Nature', 'title': 'A molecular cell atlas of the human lung from single-cell RNA sequencing.', 'authors': ['Travaglini KJ', 'Nabhan AN', 'Penland L', 'Sinha R', 'Gillich A', 'Sit RV', 'Chang S', 'Conley SD', 'Mori Y', 'Seita J', 'Berry GJ', 'Shrager JB', 'Metzger RJ', 'Kuo CS', 'Neff N', 'Weissman IL', 'Quake SR', 'Krasnow MA.']}]}
Updating project 183c7b4c-b64c-4d07-bf62-4dad77af5778: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.cell.2016.03.023', 'url': 'http://dx.doi.org/10.1016/j.cell.2016.03.023', 'journalTitle': 'Cell', 'title': 'Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.', 'authors': ['Petropoulos S', 'Edsgärd D', 'Reinius B', 'Deng Q', 'Panula SP', 'Codeluppi S', 'Plaza Reyes A', 'Linnarsson S', 'Sandberg R', 'Lanner F.']}]}
Updating project dbd836cf-bfc2-41f0-9834-41cc6c0b235a: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.immuni.2020.03.019', 'url': 'http://dx.doi.org/10.1016/j.immuni.2020.03.019', 'journalTitle': 'Immunity', 'title': 'Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.', 'authors': ['Lavaert M', 'Liang KL', 'Vandamme N', 'Park JE', 'Roels J', 'Kowalczyk MS', 'Li B', 'Ashenberg O', 'Tabaka M', 'Dionne D', 'Tickle TL', 'Slyper M', 'Rozenblatt-Rosen O', 'Vandekerckhove B', 'Leclercq G', 'Regev A', 'Van Vlierberghe P', 'Guilliams M', 'Teichmann SA', 'Saeys Y', 'Taghon T']}]}
Updating project 7ac8822c-4ef0-4194-adf0-74290611b1c6: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41587-020-0602-4', 'url': 'http://dx.doi.org/10.1038/s41587-020-0602-4', 'journalTitle': 'Nature Biotechnology', 'title': 'COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis.', 'authors': ['Chua RL', 'Lukassen S', 'Trump S', 'Hennig BP', 'Wendisch D', 'Pott F', 'Debnath O', 'Thürmann L', 'Kurth F', 'Völker MT', 'Kazmierski J', 'Timmermann B', 'Twardziok S', 'Schneider S', 'Machleidt F', 'Müller-Redetzky H', 'Maier M', 'Krannich A', 'Schmidt S', 'Balzer F', 'Liebig J', 'Loske J', 'Suttorp N', 'Eils J', 'Ishaque N', 'Liebert UG', 'von Kalle C', 'Hocke A', 'Witzenrath M', 'Goffinet C', 'Drosten C', 'Laudi S', 'Lehmann I', 'Conrad C', 'Sander LE', 'Eils R.']}]}
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Updating project ef1e3497-515e-4bbe-8d4c-10161854b699: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1164/rccm.201911-2199oc', 'url': 'http://dx.doi.org/10.1164/rccm.201911-2199oc', 'journalTitle': 'American Journal of Respiratory and Critical Care Medicine', 'title': 'A Single-Cell Atlas of the Human Healthy Airways.', 'authors': ['Deprez M', 'Zaragosi LE', 'Truchi M', 'Becavin C', 'Ruiz García S', 'Arguel MJ', 'Plaisant M', 'Magnone V', 'Lebrigand K', 'Abelanet S', 'Brau F', 'Paquet A', "Pe'er D", 'Marquette CH', 'Leroy S', 'Barbry P.']}]}
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Updating project c0518445-3b3b-49c6-b8fc-c41daa4eacba: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41591-019-0468-5', 'url': 'http://dx.doi.org/10.1038/s41591-019-0468-5', 'journalTitle': 'Nature Medicine', 'title': 'A cellular census of human lungs identifies novel cell states in health and in asthma.', 'authors': ['Vieira Braga FA', 'Kar G', 'Berg M', 'Carpaij OA', 'Polanski K', 'Simon LM', 'Brouwer S', 'Gomes T', 'Hesse L', 'Jiang J', 'Fasouli ES', 'Efremova M', 'Vento-Tormo R', 'Talavera-López C', 'Jonker MR', 'Affleck K', 'Palit S', 'Strzelecka PM', 'Firth HV', 'Mahbubani KT', 'Cvejic A', 'Meyer KB', 'Saeb-Parsy K', 'Luinge M', 'Brandsma CA', 'Timens W', 'Angelidis I', 'Strunz M', 'Koppelman GH', 'van Oosterhout AJ', 'Schiller HB', 'Theis FJ', 'van den Berge M', 'Nawijn MC', 'Teichmann SA.']}]}
Updating project 8319c26c-6fb5-40cb-b511-f50f10bf05a7: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.kint.2020.09.015', 'url': 'http://dx.doi.org/10.1016/j.kint.2020.09.015', 'journalTitle': 'Kidney International', 'title': 'SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease.', 'authors': ['Menon R', 'Otto EA', 'Sealfon R', 'Nair V', 'Wong AK', 'Theesfeld CL', 'Chen X', 'Wang Y', 'Boppana AS', 'Luo J', 'Yang Y', 'Kasson PM', 'Schaub JA', 'Berthier CC', 'Eddy S', 'Lienczewski CC', 'Godfrey B', 'Dagenais SL', 'Sohaney R', 'Hartman J', 'Fermin D', 'Subramanian L', 'Looker HC', 'Harder JL', 'Mariani LH', 'Hodgin JB', 'Sexton JZ', 'Wobus CE', 'Naik AS', 'Nelson RG', 'Troyanskaya OG', 'Kretzler M.']}]}
Updating project 0d4b87ea-6e9e-4569-82e4-1343e0e3259f: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41467-020-17800-6', 'url': 'http://dx.doi.org/10.1038/s41467-020-17800-6', 'journalTitle': 'Nature Communications', 'title': 'High throughput error corrected Nanopore single cell transcriptome sequencing.', 'authors': ['Lebrigand K', 'Magnone V', 'Barbry P', 'Waldmann R.']}]}
Updating project a7800f1b-d2d0-4a65-861f-fe1612a73162: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.cell.2020.08.003', 'url': 'http://dx.doi.org/10.1016/j.cell.2020.08.003', 'journalTitle': 'Cell', 'title': 'The Human and Mouse Enteric Nervous System at Single-Cell Resolution', 'authors': ['Drokhlyansky E', 'Smillie CS', 'Van Wittenberghe N', 'Ericsson M', 'Griffin GK', 'Dionne D', 'Cuoco MS', 'Goder-Reiser MN', 'Sharova T', 'Aguirre AJ', 'Boland GM', 'Graham D', 'Rozenblatt-Rosen O', 'Xavier RJ', 'Regev A.']}]}
Updating project 091cf39b-01bc-42e5-9437-f419a66c8a45: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41587-019-0068-4', 'url': 'http://dx.doi.org/10.1038/s41587-019-0068-4', 'journalTitle': 'Nature Biotechnology', 'title': 'Characterization of cell fate probabilities in single-cell data with Palantir', 'authors': ['Setty M', 'Kieseliovas V', 'Levine J', 'Gayoso A', 'Mazutis L', "Pe'er D"]}]}
Updating project 455b46e6-d8ea-4611-861e-de720a562ada: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.01.26.919753', 'url': 'http://dx.doi.org/10.1101/2020.01.26.919753', 'journalTitle': 'bioRxiv', 'title': 'Quantitative and molecular differences distinguish adult human medullary and extramedullary haematopoietic stem and progenitor cell landscapes.', 'authors': ['Mende N', 'Bastos H', 'Santoro A', 'Sham K', 'Mahbubani K', 'Curd A', 'Takizawa H', 'Wilson N', 'Göttgens B', 'Saeb-Parsy K', 'Laurenti E']}]}
Updating project 9c20a245-f2c0-43ae-82c9-2232ec6b594f: {'isInCatalogue': True}
Updating project 29ed62cc-8875-4c8c-b962-74670d892745: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1084/jem.20190811', 'url': 'http://dx.doi.org/10.1084/jem.20190811', 'journalTitle': 'The Journal of Experimental Medicine', 'title': 'Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation.', 'authors': ['Chen YL', 'Gomes T', 'Hardman CS', 'Vieira Braga FA', 'Gutowska-Owsiak D', 'Salimi M', 'Gray N', 'Duncan DA', 'Reynolds G', 'Johnson D', 'Salio M', 'Cerundolo V', 'Barlow JL', 'McKenzie ANJ', 'Teichmann SA', 'Haniffa M', 'Ogg G.']}]}
Updating project 85a9263b-0887-48ed-ab1a-ddfa773727b6: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.06.30.174391', 'url': 'http://dx.doi.org/10.1101/2020.06.30.174391', 'journalTitle': 'bioRxiv', 'title': 'Spatial and single-cell transcriptional landscape of human cerebellar development', 'authors': ['Aldinger KA', 'Thomson Z', 'Haldipur P', 'Deng M', 'Timms AE', 'Hirano M', 'Santpere G', 'Roco C', 'Rosenberg AB', 'Lorente-Galdos B', 'Gulden FO', 'O’Day D', 'Overman LM', 'Lisgo SN', 'Alexandre P', 'Sestan N', 'Doherty D', 'Dobyns WB', 'Seelig G', 'Glass IA', 'Millen KJ.']}]}
Updating project 769a08d1-b8a4-4f1e-95f7-6071a9827555: {'isInCatalogue': True, 'publicationsInfo': [{'doi': 'https://doi.org/10.1038/s41587-020-00796-1', 'url': 'http://dx.doi.org/10.1038/s41587-020-00796-1', 'journalTitle': 'Nature Biotechnology', 'title': 'Delayed viral clearance and exacerbated airway hyperinflammation in hypertensive COVID-19 patients', 'authors': ['Trump S', 'Lukassen S', 'Anker MS', 'Chua RL', 'Liebig J', 'Thürmann L', 'Corman VM', 'Binder M', 'Loske J', 'Klasa C', 'Krieger TG', 'Hennig BP', 'Messingschlager M', 'Pott F', 'Kazmierski J', 'Twardziok S', 'Albrecht JP', 'Eils J', 'Hadzibegovic S', 'Lena A', 'Heidecker B', 'Goffinet C', 'Kurth F', 'Witzenrath M', 'Völker MT', 'Müller SD', 'Liebert UG', 'Ishaque N', 'Kaderali L', 'Sander LE', 'Laudi S', 'Drosten C', 'Eils R', 'Conrad C', 'Landmesser U', 'Lehmann I.']}]}
Updating project 165dea71-a95a-44e1-88cd-b2d9ad68bb1e: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-019-1506-7', 'url': 'http://dx.doi.org/10.1038/s41586-019-1506-7', 'journalTitle': 'Nature', 'title': 'Conserved cell types with divergent features in human versus mouse cortex.', 'authors': ['Hodge RD', 'Bakken TE', 'Miller JA', 'Smith KA', 'Barkan ER', 'Graybuck LT', 'Close JL', 'Long B', 'Johansen N', 'Penn O', 'Yao Z', 'Eggermont J', 'Höllt T', 'Levi BP', 'Shehata SI', 'Aevermann B', 'Beller A', 'Bertagnolli D', 'Brouner K', 'Casper T', 'Cobbs C', 'Dalley R', 'Dee N', 'Ding SL', 'Ellenbogen RG', 'Fong O', 'Garren E', 'Goldy J', 'Gwinn RP', 'Hirschstein D', 'Keene CD', 'Keshk M', 'Ko AL', 'Lathia K', 'Mahfouz A', 'Maltzer Z', 'McGraw M', 'Nguyen TN', 'Nyhus J', 'Ojemann JG', 'Oldre A', 'Parry S', 'Reynolds S', 'Rimorin C', 'Shapovalova NV', 'Somasundaram S', 'Szafer A', 'Thomsen ER', 'Tieu M', 'Quon G', 'Scheuermann RH', 'Yuste R', 'Sunkin SM', 'Lelieveldt B', 'Feng D', 'Ng L', 'Bernard A', 'Hawrylycz M', 'Phillips JW', 'Tasic B', 'Zeng H', 'Jones AR', 'Koch C', 'Lein ES.']}]}
Updating project ffb57f6c-6ea1-4222-9f94-aeef9e273405: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1053/j.gastro.2020.11.010', 'url': 'http://dx.doi.org/10.1053/j.gastro.2020.11.010', 'journalTitle': 'Gastroenterology', 'title': 'Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas.', 'authors': ['Tosti L', 'Hang Y', 'Debnath O', 'Tiesmeyer S', 'Trefzer T', 'Steiger K', 'Ten FW', 'Lukassen S', 'Ballke S', 'Kühl AA', 'Spieckermann S', 'Bottino R', 'Ishaque N', 'Weichert W', 'Kim SK', 'Eils R', 'Conrad C.']}]}
Updating project 77423e58-0fbb-495a-9ec2-bd9a8010f21d: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/721258', 'url': 'http://dx.doi.org/10.1101/721258', 'journalTitle': 'bioRxiv', 'title': 'Single cell transcriptome atlas of immune cells in human small intestine and in celiac disease', 'authors': ['Atlasy N', 'Bujko A', 'Brazda PB', 'Janssen-Megens E', 'Bækkevold ES', 'Jahnsen J', 'Jahnsen FL', 'Stunnenberg HG.']}]}
Updating project 5850583c-baec-4427-8656-cd3c96c07727: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41591-020-0844-1', 'url': 'http://dx.doi.org/10.1038/s41591-020-0844-1', 'journalTitle': 'Nature Medicine', 'title': 'A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.', 'authors': ['Slyper M', 'Porter CBM', 'Ashenberg O', 'Waldman J', 'Drokhlyansky E', 'Wakiro I', 'Smillie C', 'Smith-Rosario G', 'Wu J', 'Dionne D', 'Vigneau S', 'Jané-Valbuena J', 'Tickle TL', 'Napolitano S', 'Su MJ', 'Patel AG', 'Karlstrom A', 'Gritsch S', 'Nomura M', 'Waghray A', 'Gohil SH', 'Tsankov AM', 'Jerby-Arnon L', 'Cohen O', 'Klughammer J', 'Rosen Y', 'Gould J', 'Nguyen L', 'Hofree M', 'Tramontozzi PJ', 'Li B', 'Wu CJ', 'Izar B', 'Haq R', 'Hodi FS', 'Yoon CH', 'Hata AN', 'Baker SJ', 'Suvà ML', 'Bueno R', 'Stover EH', 'Clay MR', 'Dyer MA', 'Collins NB', 'Matulonis UA', 'Wagle N', 'Johnson BE', 'Rotem A', 'Rozenblatt-Rosen O', 'Regev A.']}]}
Updating project 1fac187b-1c3f-41c4-b6b6-6a9a8c0489d1: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-020-2157-4', 'url': 'http://dx.doi.org/10.1038/s41586-020-2157-4', 'journalTitle': 'Nature', 'title': 'Construction of a human cell landscape at single-cell level.', 'authors': ['Han X', 'Zhou Z', 'Fei L', 'Sun H', 'Wang R', 'Chen Y', 'Chen H', 'Wang J', 'Tang H', 'Ge W', 'Zhou Y', 'Ye F', 'Jiang M', 'Wu J', 'Xiao Y', 'Jia X', 'Zhang T', 'Ma X', 'Zhang Q', 'Bai X', 'Lai S', 'Yu C', 'Zhu L', 'Lin R', 'Gao Y', 'Wang M', 'Wu Y', 'Zhang J', 'Zhan R', 'Zhu S', 'Hu H', 'Wang C', 'Chen M', 'Huang H', 'Liang T', 'Chen J', 'Wang W', 'Zhang D', 'Guo G.']}]}
Updating project 4ba0a537-c21b-4bc1-a54f-4ebd5fc8cf45: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.cell.2018.06.021', 'url': 'http://dx.doi.org/10.1016/j.cell.2018.06.021', 'journalTitle': 'Cell', 'title': 'Molecular Architecture of the Mouse Nervous System.', 'authors': ['Zeisel A', 'Hochgerner H', 'Lönnerberg P', 'Johnsson A', 'Memic F', 'van der Zwan J', 'Häring M', 'Braun E', 'Borm LE', 'La Manno G', 'Codeluppi S', 'Furlan A', 'Lee K', 'Skene N', 'Harris KD', 'Hjerling-Leffler J', 'Arenas E', 'Ernfors P', 'Marklund U', 'Linnarsson S.']}]}
Updating project 58028aa8-0ed2-49ca-b60f-15e2ed5989d5: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.15252/embj.20105114', 'url': 'http://dx.doi.org/10.15252/embj.20105114', 'journalTitle': 'The EMBO Journal', 'title': 'SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells', 'authors': ['Lukassen S', 'Chua RL', 'Trefzer T', 'Kahn NC', 'Schneider MA', 'Muley T', 'Winter H', 'Meister M', 'Veith C', 'Boots AW', 'Hennig BP', 'Kreuter M', 'Conrad C', 'Eils R.']}]}
Updating project d84fd289-1b4b-43f0-aa84-9f0928937106: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1161/circulationaha.120.047911', 'url': 'http://dx.doi.org/10.1161/circulationaha.120.047911', 'journalTitle': 'Circulation', 'title': 'Myocyte-Specific Upregulation of <i>ACE2</i> in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis.', 'authors': ['Tucker NR', 'Chaffin M', 'Bedi KC', 'Papangeli I', 'Akkad AD', 'Arduini A', 'Hayat S', 'Eraslan G', 'Muus C', 'Bhattacharyya RP', 'Stegmann CM', 'Human Cell Atlas Lung Biological Network', 'Margulies KB', 'Ellinor PT', 'Human Cell Atlas Lung Biological Network Consortium Members.']}]}
Updating project 6c0e3b28-5be0-45b6-9e17-809048f18284: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.04.10.022103', 'url': 'http://dx.doi.org/10.1101/2020.04.10.022103', 'journalTitle': 'bioRxiv', 'title': 'Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19', 'authors': ['Han L', 'Wei X', 'Liu C', 'Volpe G', 'Wang Z', 'Pan T', 'Yuan Y', 'Lei Y', 'Lai Y', 'Ward C', 'Yu Y', 'Wang M', 'Shi Q', 'Wu T', 'Wu L', 'Liu Y', 'Wang C', 'Zhang Y', 'Sun H', 'Yu H', 'Zhuang Z', 'Tang T', 'Huang Y', 'Lu H', 'Xu L', 'Xu J', 'Cheng M', 'Liu Y', 'Wong CW', 'Tan T', 'Ji W', 'Maxwell PH', 'Yang H', 'Wang J', 'Zhu S', 'Liu S', 'Xu X', 'Hou Y', 'Esteban MA', 'Liu L', 'South China Greater Bay Area-Single Cell Consortium (SC-GBA-C).']}]}
Updating project 69d798a1-80b3-4fc8-b124-e3a256422127: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.10.26.20219089', 'url': 'http://dx.doi.org/10.1101/2020.10.26.20219089', 'journalTitle': 'medRxiv', 'title': 'Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis', 'authors': ['Huang N', 'Perez P', 'Kato T', 'Mikami Y', 'Okuda K', 'Gilmore RC', 'Domínguez Conde C', 'Gasmi B', 'Stein S', 'Beach M', 'Pelayo E', 'Maldonado J', 'LaFont B', 'Padilla R', 'Murrah V', 'Maile R', 'Lovell W', 'Wallet S', 'Bowman NM', 'Meinig SL', 'Wolfgang MC', 'Choudhury SN', 'Novotny M', 'Aevermann BD', 'Scheuermann R', 'Cannon G', 'Anderson C', 'Marchesan J', 'Bush M', 'Freire M', 'Kimple A', 'Herr DL', 'Rabin J', 'Grazioli A', 'French BN', 'Pranzatelli T', 'Chiorini JA', 'Kleiner DE', 'Pittaluga S', 'Hewitt S', 'Burbelo PD', 'Chertow D', 'Frank K', 'Lee J', 'Boucher RC', 'Teichmann SA', 'Warner BM', 'Byrd KM', 'NIH COVID-19 Autopsy Consortium', 'HCA Oral and Craniofacial Biological Network.']}]}
Updating project 859affdc-3e85-4444-bb87-fe3887d6238c: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41591-020-0868-6', 'url': 'http://dx.doi.org/10.1038/s41591-020-0868-6', 'journalTitle': 'Nature Medicine', 'title': 'SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.', 'authors': ['Sungnak W', 'Huang N', 'Bécavin C', 'Berg M', 'Queen R', 'Litvinukova M', 'Talavera-López C', 'Maatz H', 'Reichart D', 'Sampaziotis F', 'Worlock KB', 'Yoshida M', 'Barnes JL', 'HCA Lung Biological Network.']}]}
Updating project 2d4d89f2-ebeb-467c-ae60-a3efc5e8d4ba: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.11.20.20227355', 'url': 'http://dx.doi.org/10.1101/2020.11.20.20227355', 'journalTitle': 'medRxiv', 'title': 'Single cell profiling of COVID-19 patients: an international data resource from multiple tissues', 'authors': ['Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia', 'Ballestar E', 'Farber DL', 'Glover S', 'Horwitz B', 'Meyer K', 'Nikolić M', 'Ordovas-Montanes J', 'Sims P', 'Shalek A', 'Vandamme N', 'Vandekerckhove L', 'Vento-Tormo R', 'Villani AC.']}]}
Updating project efea6426-510a-4b60-9a19-277e52bfa815: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.3389/fimmu.2021.636720', 'url': 'http://dx.doi.org/10.3389/fimmu.2021.636720', 'journalTitle': 'Frontiers in Immunology', 'title': 'Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28', 'authors': ['Lawlor N', 'Nehar-Belaid D', 'Grassmann JDS', 'Stoeckius M', 'Smibert P', 'Stitzel ML', 'Pascual V', 'Banchereau J', 'Williams A', 'Ucar D']}]}
Updating project 0406796c-5a6e-4eeb-b6e4-12de1e659bd9: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.08.29.272831', 'url': 'http://dx.doi.org/10.1101/2020.08.29.272831', 'journalTitle': 'bioRxiv', 'title': 'Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram', 'authors': ['Biancalani T', 'Scalia G', 'Buffoni L', 'Avasthi R', 'Lu Z', 'Sanger A', 'Tokcan N', 'Vanderburg CR', 'Segerstolpe A', 'Zhang M', 'Avraham-Davidi I', 'Vickovic S', 'Nitzan M', 'Ma S', 'Buenrostro J', 'Brown NB', 'Fanelli D', 'Zhuang X', 'Macosko EZ', 'Regev A.']}]}
Updating project daf9d982-7ce6-43f6-ab51-272577290606: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1164/rccm.201712-2410oc', 'url': 'http://dx.doi.org/10.1164/rccm.201712-2410oc', 'journalTitle': 'American Journal of Respiratory and Critical Care Medicine', 'title': 'Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis.', 'authors': ['Reyfman PA', 'Walter JM', 'Joshi N', 'Anekalla KR', 'McQuattie-Pimentel AC', 'Chiu S', 'Fernandez R', 'Akbarpour M', 'Chen CI', 'Ren Z', 'Verma R', 'Abdala-Valencia H', 'Nam K', 'Chi M', 'Han S', 'Gonzalez-Gonzalez FJ', 'Soberanes S', 'Watanabe S', 'Williams KJN', 'Flozak AS', 'Nicholson TT', 'Morgan VK', 'Winter DR', 'Hinchcliff M', 'Hrusch CL', 'Guzy RD', 'Bonham CA', 'Sperling AI', 'Bag R', 'Hamanaka RB', 'Mutlu GM', 'Yeldandi AV', 'Marshall SA', 'Shilatifard A', 'Amaral LAN', 'Perlman H', 'Sznajder JI', 'Argento AC', 'Gillespie CT', 'Dematte J', 'Jain M', 'Singer BD', 'Ridge KM', 'Lam AP', 'Bharat A', 'Bhorade SM', 'Gottardi CJ', 'Budinger GRS', 'Misharin AV.']}]}
Updating project 30d5c857-9d46-465b-9fd8-236ff31f2f5a: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.01.21.20018358', 'url': 'http://dx.doi.org/10.1101/2020.01.21.20018358', 'journalTitle': 'medRxiv', 'title': 'Integrated single cell analysis of human lung fibrosis resolves cellular origins of predictive protein signatures in body fluids', 'authors': ['Mayr CH', 'Simon LM', 'Leuschner G', 'Ansari M', 'Geyer PE', 'Angelidis I', 'Strunz M', 'Singh P', 'Kneidinger N', 'Reichenberger F', 'Silbernagel E', 'Böhm S', 'Adler H', 'Hilgendorff A', 'Lindner M', 'Prasse A', 'Behr J', 'Mann M', 'Eickelberg O', 'Theis FJ', 'Schiller HB.']}]}
Updating project e4b2e4d9-2b9b-46cf-b0e0-bb23ff28030a: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.06.14.151167', 'url': 'http://dx.doi.org/10.1101/2020.06.14.151167', 'journalTitle': 'bioRxiv', 'title': 'Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney', 'authors': ['Muto Y', 'Wilson PC', 'Wu H', 'Waikar SS', 'Humphreys BD.']}]}
Updating project d363d09f-924b-43dd-9634-6988f1e46db2: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.06.25.171793', 'url': 'http://dx.doi.org/10.1101/2020.06.25.171793', 'journalTitle': 'bioRxiv', 'title': 'A single cell atlas of the healthy breast tissues reveal clinically relevant clusters of breast epithelial cells', 'authors': ['Bhat-Nakshatri P', 'Gao H', 'McGuire PC', 'Xuei X', 'Sheng L', 'Wan J', 'Liu Y', 'Althouse SK', 'Colter A', 'Sandusky G', 'Storniolo AM', 'Nakshatri H.']}]}
Updating project 2bda737d-bd81-412f-b37b-cf76b059f778: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41467-019-13382-0', 'url': 'http://dx.doi.org/10.1038/s41467-019-13382-0', 'journalTitle': 'Nature Communications', 'title': 'Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation.', 'authors': ['Subramanian A', 'Sidhom EH', 'Emani M', 'Vernon K', 'Sahakian N', 'Zhou Y', 'Kost-Alimova M', 'Slyper M', 'Waldman J', 'Dionne D', 'Nguyen LT', 'Weins A', 'Marshall JL', 'Rosenblatt-Rosen O', 'Regev A', 'Greka A.']}]}
Updating project 87e600d2-57ca-4f16-addd-d357ab2f24ee: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.devcel.2020.01.033', 'url': 'http://dx.doi.org/10.1016/j.devcel.2020.01.033', 'journalTitle': 'Developmental Cell', 'title': 'In\xa0Vitro and In\xa0Vivo Development of the Human Airway at Single-Cell Resolution.', 'authors': ['Miller AJ', 'Yu Q', 'Czerwinski M', 'Tsai YH', 'Conway RF', 'Wu A', 'Holloway EM', 'Walker T', 'Glass IA', 'Treutlein B', 'Camp JG', 'Spence JR.']}]}
Updating project fc934a13-4a98-4901-8208-590534cd7b87: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.stem.2020.11.008', 'url': 'http://dx.doi.org/10.1016/j.stem.2020.11.008', 'journalTitle': 'Cell Stem Cell', 'title': 'Mapping Development of the Human Intestinal Niche at Single-Cell Resolution.', 'authors': ['Holloway EM', 'Czerwinski M', 'Tsai YH', 'Wu JH', 'Wu A', 'Childs CJ', 'Walton KD', 'Sweet CW', 'Yu Q', 'Glass I', 'Treutlein B', 'Camp JG', 'Spence JR.']}]}
Updating project a6ac6702-1938-436f-8437-67d08161fdeb: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1101/2020.07.24.219147', 'url': 'http://dx.doi.org/10.1101/2020.07.24.219147', 'journalTitle': 'bioRxiv', 'title': 'An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine', 'authors': ['Yu Q', 'Kilik U', 'Holloway EM', 'Tsai Y', 'Wu A', 'Wu JH', 'Czerwinski M', 'Childs C', 'He Z', 'Glass IA', 'Higgins PDR', 'Treutlein B', 'Spence JR', 'Camp JG.']}]}
Updating project c535ac1f-1902-43bc-86a5-1e1643a5578e: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.devcel.2020.07.023', 'url': 'http://dx.doi.org/10.1016/j.devcel.2020.07.023', 'journalTitle': 'Developmental Cell', 'title': 'Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells.', 'authors': ['Holloway EM', 'Wu JH', 'Czerwinski M', 'Sweet CW', 'Wu A', 'Tsai YH', 'Huang S', 'Stoddard AE', 'Capeling MM', 'Glass I', 'Spence JR.']}]}
Updating project 08fb10df-32e5-456c-9882-e33fcd49077a: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41591-020-0901-9', 'url': 'http://dx.doi.org/10.1038/s41591-020-0901-9', 'journalTitle': 'Nature Medicine', 'title': 'Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.', 'authors': ['Liao M', 'Liu Y', 'Yuan J', 'Wen Y', 'Xu G', 'Zhao J', 'Cheng L', 'Li J', 'Wang X', 'Wang F', 'Liu L', 'Amit I', 'Zhang S', 'Zhang Z.']}]}
Updating project f71d4ab7-8115-4208-83b6-bf03dec07b74: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41467-018-04334-1', 'url': 'http://dx.doi.org/10.1038/s41467-018-04334-1', 'journalTitle': 'Nature Communications', 'title': 'Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity.', 'authors': ['Nguyen QH', 'Pervolarakis N', 'Blake K', 'Ma D', 'Davis RT', 'James N', 'Phung AT', 'Willey E', 'Kumar R', 'Jabart E', 'Driver I', 'Rock J', 'Goga A', 'Khan SA', 'Lawson DA', 'Werb Z', 'Kessenbrock K.']}]}
Updating project fa3f460f-4fb9-4ced-b548-8ba6a8ecae3f: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.cell.2020.12.016', 'url': 'http://dx.doi.org/10.1016/j.cell.2020.12.016', 'journalTitle': 'Cell', 'title': 'Spatiotemporal analysis of human intestinal development at single-cell resolution.', 'authors': ['Fawkner-Corbett D', 'Antanaviciute A', 'Parikh K', 'Jagielowicz M', 'Gerós AS', 'Gupta T', 'Ashley N', 'Khamis D', 'Fowler D', 'Morrissey E', 'Cunningham C', 'Johnson PRV', 'Koohy H', 'Simmons A.']}]}
Updating project c893cb57-5c9f-4f26-9312-21b85be84313: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-019-0992-y', 'url': 'http://dx.doi.org/10.1038/s41586-019-0992-y', 'journalTitle': 'Nature', 'title': 'Colonic epithelial cell diversity in health and inflammatory bowel disease.', 'authors': ['Parikh K', 'Antanaviciute A', 'Fawkner-Corbett D', 'Jagielowicz M', 'Aulicino A', 'Lagerholm C', 'Davis S', 'Kinchen J', 'Chen HH', 'Alham NK', 'Ashley N', 'Johnson E', 'Hublitz P', 'Bao L', 'Lukomska J', 'Andev RS', 'Björklund E', 'Kessler BM', 'Fischer R', 'Goldin R', 'Koohy H', 'Simmons A']}]}
Updating project 16ed4ad8-7319-46b2-8859-6fe1c1d73a82: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.stem.2018.10.010', 'url': 'http://dx.doi.org/10.1016/j.stem.2018.10.010', 'journalTitle': 'Cell Stem Cell', 'title': 'Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics.', 'authors': ['Wu H', 'Uchimura K', 'Donnelly EL', 'Kirita Y', 'Morris SA', 'Humphreys BD']}]}
Updating project 41fb1734-a121-4616-95c7-3b732c9433c7: {'isInCatalogue': True}
Updating project 1c6a960d-52ac-44ea-b728-a59c7ab9dc8e: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.celrep.2019.02.043', 'url': 'http://dx.doi.org/10.1016/j.celrep.2019.02.043', 'journalTitle': 'Cell Reports', 'title': 'Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes.', 'authors': ['Fang Z', 'Weng C', 'Li H', 'Tao R', 'Mai W', 'Liu X', 'Lu L', 'Lai S', 'Duan Q', 'Alvarez C', 'Arvan P', 'Wynshaw-Boris A', 'Li Y', 'Pei Y', 'Jin F', 'Li Y']}]}
Updating project b3938158-4e8d-4fdb-9e13-9e94270dde16: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1053/j.gastro.2020.11.010 ', 'url': 'http://dx.doi.org/10.1053/j.gastro.2020.11.010', 'journalTitle': 'Gastroenterology', 'title': 'Single-Nucleus and In Situ RNA-Sequencing Reveal Cell Topographies in the Human Pancreas.', 'authors': ['Tosti L', 'Hang Y', 'Debnath O', 'Tiesmeyer S', 'Trefzer T', 'Steiger K', 'Ten FW', 'Lukassen S', 'Ballke S', 'Kühl AA', 'Spieckermann S', 'Bottino R', 'Ishaque N', 'Weichert W', 'Kim SK', 'Eils R', 'Conrad C']}]}
Updating project 51f40ab7-e7b2-4cad-9a62-b02ea044442c: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.cell.2019.08.008', 'url': 'http://dx.doi.org/10.1016/j.cell.2019.08.008', 'journalTitle': 'Cell', 'title': "Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy.", 'authors': ['Martin JC', 'Chang C', 'Boschetti G', 'Ungaro R', 'Giri M', 'Grout JA', 'Gettler K', 'Chuang LS', 'Nayar S', 'Greenstein AJ', 'Dubinsky M', 'Walker L', 'Leader A', 'Fine JS', 'Whitehurst CE', 'Mbow ML', 'Kugathasan S', 'Denson LA', 'Hyams JS', 'Friedman JR', 'Desai PT', 'Ko HM', 'Laface I', 'Akturk G', 'Schadt EE', 'Salmon H', 'Gnjatic S', 'Rahman AH', 'Merad M', 'Cho JH', 'Kenigsberg E']}]}
Updating project 9d97f01f-9313-416e-9b07-560f048b2350: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1016/j.celrep.2018.08.056', 'url': 'http://dx.doi.org/10.1016/j.celrep.2018.08.056', 'journalTitle': 'Cell Reports', 'title': 'Targeted Therapy guided by single cell Transcriptomic analysis in drug induced induced hypersensitivity syndrome', 'authors': ['Kim D', 'Kobayashi T', 'Voison B', 'JoJ H', 'Sakamoto K', 'Jin SP', 'Kelly M', 'Pasieka HB', 'Naff JL', 'Meyerle JH', 'Ikpeama ID', 'Fahle GA', 'Davis FP', 'Rosenzweig SD', 'Alejo JC', 'Pittaluga S', 'Hong HH', 'Freeman AF', 'Nagao K', '']}]}
Updating project ce7b12ba-664f-4f79-8fc7-3de6b1892183: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1038/s41586-019-1404-z', 'url': 'http://dx.doi.org/10.1038/s41586-019-1404-z', 'journalTitle': 'Nature', 'title': 'Neuronal vulnerability and multilineage diversity in multiple sclerosis.', 'authors': ['Schirmer L', 'Velmeshev D', 'Holmqvist S', 'Kaufmann M', 'Werneburg S', 'Jung D', 'Vistnes S', 'Stockley JH', 'Young A', 'Steindel M', 'Tung B', 'Goyal N', 'Bhaduri A', 'Mayer S', 'Engler JB', 'Bayraktar OA', 'Franklin RJM', 'Haeussler M', 'Reynolds R', 'Schafer DP', 'Friese MA', 'Shiow LR', 'Kriegstein AR', 'Rowitch DH']}]}
Updating project d3a4ceac-4d66-4984-9704-2570c0647a56: {'isInCatalogue': True, 'publicationsInfo': [{'doi': '10.1126/sciimmunol.abb8786', 'url': 'http://dx.doi.org/10.1126/sciimmunol.abb8786', 'journalTitle': 'Science Immunology', 'title': 'Transcriptomic and clonal characterization of T cells in the human central nervous system.', 'authors': ['Pappalardo JL', 'Zhang L', 'Pecsok MK', 'Perlman K', 'Zografou C', 'Raddassi K', 'Abulaban A', 'Krishnaswamy S', 'Antel J', 'van Dijk D', 'Hafler DA']}]}We can now also set the publications for these 12 projects manually, even though the projects "in ingest" have no publication info:
These 3 have no Project MetaData:
This has some project metadata see- https://contribute.data.humancellatlas.org/projects/detail?uuid=005d611a-14d5-4fbf-846e-571a1f874f70 and should be included in the project catalogue. It was wrangled by Mallory so unsure why/how/if there is a discrepancy between the API and UI!?
https://contribute.data.humancellatlas.org/projects/detail?uuid=cc95ff89-2e68-4a08-a234-480eca21ce79 Another DCP1 project that should be included, again seems to have appropriate metadata
https://contribute.data.humancellatlas.org/projects/detail?uuid=fc55bd4a-8694-4a28-9a35-59a685bda323 Again there is project metadata via the UI and this should be included in the project catalogue
These 9 have no publication info:
Its fine if they have no publication details they should still be included in the catalogue
- 4a95101c-9ffc-4f30-a809-f04518a23803
- b176d756-62d8-4933-83a4-8b026380262f
- 9c20a245-f2c0-43ae-82c9-2232ec6b594f
- 41fb1734-a121-4616-95c7-3b732c9433c7
- f86f1ab4-1fbb-4510-ae35-3ffd752d4dfc
- 74b6d569-3b11-42ef-b6b1-a0454522b4a0
- f83165c5-e2ea-4d15-a5cf-33f3550bffde
- fc232d87-7b10-47f7-9197-b2c6cf210dea
- 116965f3-f094-4769-9d28-ae675c1b569c
clairerye
commented
3 years ago Project UUIDs that were in the old version of the catalogue that do not exist in ingest:
- 592a97ab-d575-4e91-b68e-547d1d66d087 Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns is now https://contribute.data.humancellatlas.org/projects/detail?uuid=cddab57b-6868-4be4-806f-395ed9dd635a Can we please check cddab57b-6868-4be4-806f-395ed9dd635a is part of the project catalogue and if not include it
- 2dcc3807-e008-4ccc-b000-bffe2d86f429 An Atlas of Immune Cell Exhaustion in HIV-Infected Individuals Revealed by Single-Cell Transcriptomics. is now https://contribute.data.humancellatlas.org/projects/detail?uuid=0fd8f918-62d6-4b8b-ac35-4c53dd601f71 so can we please check 0fd8f918-62d6-4b8b-ac35-4c53dd601f71 is part of project catalogue and include it if not.
- 9cd9669b-55cf-4b32-9187-629bcc2f7bf8 RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes - is now https://contribute.data.humancellatlas.org/projects/detail?uuid=7adede6a-0ab7-45e6-9b67-ffe7466bec1f so can we check that 7adede6a-0ab7-45e6-9b67-ffe7466bec1f is included in the project catalogue
jacobwindsor
commented
3 years ago Updated script that updates the wrangling state if a project is in DCP. Also in this gist
import argparse, json, requests
def get_publications_journal(publications):
# Use crossref API to get extra meta info
# This should be replicated in ingest API endpoint when we have an endpoint
# Not done on client side for speed
results = []
for publication in publications:
try:
crossref = requests.get(f"https://api.crossref.org/works/{publication['doi']}").json()['message']
if len(crossref['container-title']) > 0:
journal_title = crossref['container-title'][0]
elif "name" in crossref['institution']:
journal_title = crossref['institution']['name']
else:
journal_title = crossref['publisher']
results.append({
"doi": publication['doi'],
"url": crossref['URL'],
"journalTitle": journal_title,
"title": publication['title'],
"authors": publication['authors']
})
except:
print(f"Something went wrong retrieving metainformation for publication {publication['doi']}")
return results
def is_in_dcp(uuid):
azul_proj_url = f'https://service.azul.data.humancellatlas.org/index/projects/{uuid}'
if requests.get(azul_proj_url):
return True
return False
def get_project(uuid, base_url):
project_url = f'{base_url}/projects/search/findByUuid?uuid={uuid}'
try:
response = requests.get(project_url)
response.raise_for_status()
return response.json()
except Exception as e:
print(f'Error getting project {uuid}: {e}')
def patch_project(uuid, project, token):
project_patch = {}
if project["isInCatalogue"] == False:
project_patch["isInCatalogue"] = True
if "publications" in project["content"]:
project_patch["publicationsInfo"] = get_publications_journal(project["content"]["publications"])
if is_in_dcp(uuid):
project_patch["wranglingState"] = "Published in DCP"
if not project_patch:
print(f"Patch unnecessary for project UUID: {uuid}")
return None
try:
print(f"Updating project {uuid}: {project_patch}")
update_url = f'{project["_links"]["self"]["href"]}?partial=true'
headers={'Authorization': token, 'Content-Type': 'application/json'}
data = json.dumps(project_patch)
r = requests.patch(update_url, data=data, headers=headers)
r.raise_for_status()
except Exception as e:
print(f'Error patching project {uuid}: {e}')
def get_uuids(input_file):
with open(input_file, "r") as file:
return file.read().splitlines()
def get_token(input_file):
with open(input_file, "r") as file:
return file.read()
if __name__ == "__main__":
description = "Update projects in ingest to use the project catalogue and add publicationsInfo"
parser = argparse.ArgumentParser(description=description)
parser.add_argument("-i", "--input", help="File containing a list of UUIDs to scrape. Each UUID must be on a new line.", default="published_uuids.txt")
parser.add_argument("-u", "--url", help="Base URL for Ingest API", default="https://api.ingest.dev.archive.data.humancellatlas.org")
parser.add_argument("-t", "--token", help="Text file containing an ingest token", default="token.txt")
args = parser.parse_args()
uuids = get_uuids(args.input)
token = get_token(args.token)
for uuid in uuids:
project = get_project(uuid, args.url)
if project:
patch_project(uuid, project, token)
Aim: improve the maintainability of the project catalogue, allowing it to grow without causing an increasing amount of development overhead. Currently, it is populated via a manually run script that consumes the ingest API this was a proof of concept solution that now needs to be replaced by a sustainable solution.
sub tasks summary (Update 25/05)
Ingest-Core:
ingest-core#65 Merged to Dev
ingest-core#66 Merged to Dev
Project-Index
Ingest UI:
ingest-ui#93 In Review
Operations