Project Catalogue entries without Publications

[MightyAx]

The following 17 projects present in the Catalogue are missing their publication information

Unique Key  Date added  Project Title   Publications    Authors Organs  Technologies    Cell count  ENA Arrayexpress    GEO EGA dbGaP   HCA Data Portal URL
6768e2c1-38ce-4b07-87d5-552d52f01a30    30/11/2021  Single-cell RNA sequencing of urinary cells reveals distinct cellular diversity in COVID-19- associated AKI         bladder organ   10x 3' v2               GSE180595           
2b38025d-a5ea-4c0f-b22e-367824bcaf4c    21/10/2021  Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro         uterus  10x 3' v2, 10x 3' v3    55000   ERP128125, ERP127889    E-MTAB-10287, E-MTAB-10283              https://data.humancellatlas.org/explore/projects/2b38025d-a5ea-4c0f-b22e-367824bcaf4c
fde199d2-a841-4ed1-aa65-b9e0af8969b1    20/09/2021  Cells of the human intestinal tract mapped across space and time            large intestine, small intestine, vermiform appendix    Visium Spatial Gene Expression, 10x 5' v2   428000      E-MTAB-9543, E-MTAB-9536, E-MTAB-9532, E-MTAB-9533, E-MTAB-10386                
4c886170-3f73-4661-832f-ab10409e84a9    21/06/2021  COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.           lung, kidney, liver, heart  10x 3' v3   106792          GSE171668           
a0b4a252-c768-44df-a82a-399413a75ec1    17/06/2021  Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers.         lung    Drop-seq    233638                      
0061c7e8-7b90-4296-be53-ca1de3bd6651    16/06/2021  A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2         lung, kidney, liver, spleen, trachea, lymph node, muscle tissue, nasal cavity mucosa, oral epithelium, brain    10x 3' v3, 10x 5' v2, RNAscope  220023          GSE171668, GSE163530            
e9f36305-d857-44a3-93f0-df4e6007dc97    16/06/2021  Spatial multi-omic map of human myocardial infarction           heart   Visium Spatial Gene Expression  12184                       
1538d572-bcb7-426b-8d2c-84f3a7f87bb0    16/06/2021  The local and systemic response to SARS-CoV-2 infection in children and adults          blood, respiratory tract    10x immune profiling    468214          GSE168215           
60ea42e1-af49-42f5-8164-d641fdb696bc    11/06/2021  A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva          saliva  Smart-seq2  1145    SRP271375                   https://data.humancellatlas.org/explore/projects/60ea42e1-af49-42f5-8164-d641fdb696bc
910fc0b2-3054-47b2-97f0-549f23e29d72    11/06/2021  Single cell analysis of emergent haematopoiesis in the human fetal bone marrow          bone marrow Smart-seq2, CITE-seq, 10x 3' v2, 10x 3' v1      ERP123145, ERP125305    E-MTAB-9389, E-MTAB-9801                
1ce3b3dc-02f2-44a8-96da-d6d107b27a76    11/06/2021  Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells         umbilical cord  Smart-seq2  420 SRP110699       GSE100618           https://data.humancellatlas.org/explore/projects/1ce3b3dc-02f2-44a8-96da-d6d107b27a76
cc95ff89-2e68-4a08-a234-480eca21ce79    02/06/2021  Census of Immune Cells          blood, bone marrow  10x 3' v2   528092  ERP122984                   https://data.humancellatlas.org/explore/projects/cc95ff89-2e68-4a08-a234-480eca21ce79
005d611a-14d5-4fbf-846e-571a1f874f70    02/06/2021  Assessing the relevance of organoids to model inter-individual variation            skin of body, stem cell, brain  10x 3' v2   19916   ERP114427                   https://data.humancellatlas.org/explore/projects/005d611a-14d5-4fbf-846e-571a1f874f70
9c20a245-f2c0-43ae-82c9-2232ec6b594f    27/05/2021  Transcriptomic classification of human retinal cell types with single-nuclei RNA-seq.           eye 10x 3' v3   230800                      https://data.humancellatlas.org/explore/projects/9c20a245-f2c0-43ae-82c9-2232ec6b594f
fc232d87-7b10-47f7-9197-b2c6cf210dea    27/05/2021  Human Developmental Cell Atlas Sweden           brain, lung, heart  10x 3' v3                   EGAS00001004375     
b176d756-62d8-4933-83a4-8b026380262f    27/05/2021  Single-cell transcriptional landscape of human embryonic limb development           hindlimb    10x 3' v2   27426   ERP119958   E-MTAB-8813             
116965f3-f094-4769-9d28-ae675c1b569c    27/05/2021  Single cell profiling of human induced dendritic cells generated by direct reprogramming of embryonic fibroblasts           skin of body, embryo, immune system 10x 3' v2   6263    ERP120400                   https://data.humancellatlas.org/explore/projects/116965f3-f094-4769-9d28-ae675c1b569c

[ESapenaVentura]

Acceptance criteria

• [ ] The reason why the projects are displaying publication information is determined for all projects
  • 2 main reasons:
    • No DOI
    • Other (There is DOI, but publication info is not being loaded)
• [ ] Actions to solve these issues are taken

[ofanobilbao]

Probably this will need re-assessing as with the promotion to production of a fix for projects that were not correctly showing the contributor information, the Catalogue no longer displays projects that do not have a DOI in Ingest. So this ticket might as well not be longer needed

[idazucchi]

I'm going through the projects, and some have disappeared from the catalogue because they are missing the DOI My plan is to add it and hopefully they will be displayed correctly in the catalogue

DOI present in ingest

• [ ] ingest Single-cell RNA sequencing of urinary cells reveals distinct cellular diversity in COVID-19- associated AKI - uuid is wrong, UCSC - the catalogue is not checked so it's never going to show up
• [x] ingest Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
• [x] ingest Cells of the human intestinal tract mapped across space and time
• [x] ingest COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.
• [x] ingest Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers. - empty duplicate project!
• [x] ingest A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
• [x] ingest Spatial multi-omic map of human myocardial infarction
• [x] ingest The local and systemic response to SARS-CoV-2 infection in children and adults
• [x] ingest A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva - not showing up - don't know why
• [ ] ingest Single cell analysis of emergent haematopoiesis in the human fetal bone marrow - empty duplicate for a project that has already been published - delete?
• [x] ingest Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells
• [ ] ingest Census of Immune Cells - DCP1 missing publication info entirely
• [x] ingest Assessing the relevance of organoids to model inter-individual variation
• [ ] ingest Transcriptomic classification of human retinal cell types with single-nuclei RNA-seq. - lattice team - Rui Chen dataset no publication available yet
• [ ] ingest Human Developmental Cell Atlas Sweden - no publication available, in contact with the authors
• [ ] ingest Single-cell transcriptional landscape of human embryonic limb development - Peng's dataset, no publication
• [ ] ingest Single cell profiling of human induced dendritic cells generated by direct reprogramming of embryonic fibroblasts published in DCP but missing publication

[idazucchi]

Showing up in the project catalogue:

• [x] ingest Single-cell RNA sequencing of urinary cells reveals distinct cellular diversity in COVID-19- associated AKI - UCSC - added to the catalogue
• [x] ingest Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
• [x] ingest Cells of the human intestinal tract mapped across space and time
• [x] ingest COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. - [x] ingest Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers. - empty duplicate project!
• [x] ingest A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
• [x] ingest Spatial multi-omic map of human myocardial infarction
• [x] ingest The local and systemic response to SARS-CoV-2 infection in children and adults
• [x] ingest A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva - it wan't showing up because of a missing information institution from CrossRef - [ ] ingest Single cell analysis of emergent haematopoiesis in the human fetal bone marrow - empty duplicate for a project that has already been published - delete?
• [x] ingest Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells
• [x] ingest Census of Immune Cells - DCP1 missing publication info entirely
• [x] ingest Assessing the relevance of organoids to model inter-individual variation
• [x] ingest Transcriptomic classification of human retinal cell types with single-nuclei RNA-seq. - lattice team - Rui Chen dataset no publication available yet
• [x] ingest Human Developmental Cell Atlas Sweden - no publication available, in contact with the authors
• [x] ingest Single-cell transcriptional landscape of human embryonic limb development - Peng's dataset, no publication
• [x] ingest Single cell profiling of human induced dendritic cells generated by direct reprogramming of embryonic fibroblasts - published in DCP but missing publication

[gabsie]

@jacobwindsor to send his list of projects and we identify why the above behaviours. we might need to revise the filters for appearance for catalogue, with regard to missing DOI/publication. (gabs)

[idazucchi]

how long does it take for the projects to show up in the catalogue after the doi has been added to ingest?

[jacobwindsor]

I have fixed the issue with those not shown because of missing DOIs in this PR

[jacobwindsor]

List of uuids without DOIs:

cc95ff89-2e68-4a08-a234-480eca21ce79
9c20a245-f2c0-43ae-82c9-2232ec6b594f
116965f3-f094-4769-9d28-ae675c1b569c
b176d756-62d8-4933-83a4-8b026380262f
fc232d87-7b10-47f7-9197-b2c6cf210dea
1ce3b3dc-02f2-44a8-96da-d6d107b27a76
60ea42e1-af49-42f5-8164-d641fdb696bc
fde199d2-a841-4ed1-aa65-b9e0af8969b1
2b38025d-a5ea-4c0f-b22e-367824bcaf4c

FYI @idazucchi @gabsie you can see this list yourself by opening the developer tools on the project catalogue.Any projects which aren't shown due to an error are shown their with the error and the UUID.

@idazucchi the script runs at 11:00PM every night so the day after you will see it in the catalogue.

[jacobwindsor]

@idazucchi The fix is now in production

[gabsie]

2 extra projects to take a look at, for @jacobwindsor cc @idazucchi

[idazucchi]

I've added the doi to two projects ( ingest and ingest ) were already published in the DCP. I've exported the just the metadata to make sure that project information in the DCP is up to date