Update README.md

README.md

@@ -4,7 +4,7 @@ license: cc-by-4.0
 tags:
 - chemistry
 - biology
-pretty_name: "Microbiome Immunity Project Protein Universe"
+pretty_name: "Microbiome Immunity Project: Protein Universe"
 dataset_summary: >-
   ~200,000 predicted structures for diverse protein sequences from 1,003
   representative genomes across the microbial tree of life and annotate
@@ -57,27 +57,53 @@ citation_apa: >-
 size_categories:
 - 100k<n<1M
 ---
-# Dataset Card for {{ pretty_name }}
-{{ dataset_summary }}
+# Microbiome Immunity Project: Protein Universe
+~200,000 predicted structures for diverse protein sequences from 1,003
+representative genomes across the microbial tree of life and annotate
+them functionally on a per-residue basis.
 
 ## Dataset Details
 
 ### Dataset Description
+Large-scale structure prediction on representative protein domains from
+the Genomic Encyclopedia of Bacteria and Archaea (GEBA1003) reference
+genome database across the microbial tree of life. From a non-redundant
+GEBA1003 gene catalog protein sequences without matches to any structural databases
+and which produced multiple-sequence alignments of N_eff > 16 and all
+putative novel domains between 40 and 200 residues were extracted.
+For each sequence 20,000 Rosetta de novo models and up to 5 DMPfold models
+were generated. The initial output dataset (MIP_raw) of about 240,000
+models were curated to high-quality models comprising about 75% of the
+original dataset (MIP_curated). Functional annotations of the entire
+dataset were created using structure-based Graph Convolutional Network
+embeddings from DeepFRI.
+
+- **Acknowledgements:**
+  We kindly acknowledge the support of the IBM World Community Grid team
+  (Caitlin Larkin, Juan A Hindo, Al Seippel, Erika Tuttle, Jonathan D Armstrong,
+  Kevin Reed, Ray Johnson, and Viktors Berstis), and the community of 790,000
+  volunteers who donated 140,661 computational years since Aug 2017 of their
+  computer time over the course of the project. This research was also
+  supported in part by PLGrid Infrastructure (to PS). The authors thank Hera
+  Vlamakis and Damian Plichta from the Broad Institute for helpful discussions.
+  The work was supported by the Flatiron Institute as part of the Simons Foundation
+  to J.K.L., P.D.R., V.G., D.B., C.C., A.P., N.C., I.F., and R.B. This research
+  was also supported by grants NAWA PPN/PPO/2018/1/00014 to P.S. and T.K.,
+  PLGrid to P.S., and NIH - DK043351 to T.V. and R.J.X.
 
-<!-- Provide a longer summary of what this dataset is. -->
-
-{{ dataset_description }}
-
-- **Acknowledgements:** {{ acknowledgements })}
-- **Language(s) (NLP):** {{ language }}
-- **License:** {{ license }}
+- **License:** cc-by-4.0
 
 ### Dataset Sources [optional]
 
 <!-- Provide the basic links for the dataset. -->
 
-- **Repository:** {{ repo | default("[More Information Needed]", true)}}
-- **Paper [optional]:** {{ citation_apa | default("[More Information Needed]", true)}}
+- **Repository:** https://github.com/microbiome-immunity-project/protein_universe
+- **Paper:**
+  Koehler Leman, J., Szczerbiak, P., Renfrew, P. D., Gligorijevic, V., Berenberg,
+  D., Vatanen, T., … Kosciolek, T. (2023). Sequence-structure-function relationships
+  in the microbial protein universe. Nature Communications, 14(1), 2351.
+  doi:10.1038/s41467-023-37896-w
+
 
 ## Uses
 
@@ -187,4 +213,6 @@ size_categories:
 
 ## Dataset Card Contact
 
-{{ dataset_card_contact | default("[More Information Needed]", true)}}
+{{ dataset_card_contact | default("[More Information Needed]", true)}}
+
+-->