Update README.md

README.md

@@ -47,7 +47,7 @@ citation_bibtex: >-
     publisher = {Springer Science and Business Media LLC},
     author = {Koehler Leman,  Julia and Szczerbiak,  Pawel and Renfrew,  P. Douglas and Gligorijevic,  Vladimir and Berenberg,  Daniel and Vatanen,  Tommi and Taylor,  Bryn C. and Chandler,  Chris and Janssen,  Stefan and Pataki,  Andras and Carriero,  Nick and Fisk,  Ian and Xavier,  Ramnik J. and Knight,  Rob and Bonneau,  Richard and Kosciolek,  Tomasz},
     year = {2023},
-    month = apr 
+    month = apr
   }
 citation_apa: >-
   Koehler Leman, J., Szczerbiak, P., Renfrew, P. D., Gligorijevic, V., Berenberg,
@@ -74,8 +74,12 @@ 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
+original dataset (MIP_curated): Models were filtered out if (1) Rosetta
+models had >60% coil content or DMPFold models with >80% coil content,
+(2) the averaging the pairwise TM-scores of the 10 lowest-scoring models
+was less than 0.4, and (3) if the Rosetta and DMPfold models had TM-score
+less than 0.5. Functional annotations of the entire dataset were
+created using structure-based Graph Convolutional Network
 embeddings from DeepFRI.
 
 - **Acknowledgements:**
@@ -103,37 +107,37 @@ embeddings from DeepFRI.
   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
+- **Zenodo Repository:** https://doi.org/10.5281/zenodo.6611431
 
 
 ## Uses
-
-<!-- Address questions around how the dataset is intended to be used. -->
+Exploration of sequence-structure-function relationship in naturally ocurring proteins.
+The MIP database is complementary to and distinct from the other large-scale predicted
+protein structure databases such as the EBI AlphaFold database because it consists of
+proteins from Archaea and Bacteria, whose protein sequences are generally shorter
+than Eukaryotic.
 
 ### Direct Use
+This dataset could be used to
 
-<!-- This section describes suitable use cases for the dataset. -->
+-
 
-{{ direct_use | default("[More Information Needed]", true)}}
 
 ### Out-of-Scope Use
 
-<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. -->
-
-{{ out_of_scope_use | default("[More Information Needed]", true)}}
+While this dataset has been curated for quality, in some cases the predicted structures
+may not represent physically realistic conformations. Thus caution much be used when using
+it as training data for protein structure prediction and design.
 
 ## Dataset Structure
 
-<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. -->
-
-{{ dataset_structure | default("[More Information Needed]", true)}}
-
-## Dataset Creation
-
-### Curation Rationale
+    microbiome_immunity_project_dataset
+      dataset
+        dmpfold_high_quality_function_predictions
+          DeepFRI_MIP_<chunk-index>_<gene-ontology-prefix>_pred_scores.json.gz
+        dmpfold_high_quality_models
+          MIP_<MIP-ID>.pdb.gz.pdb.gz
 
-<!-- Motivation for the creation of this dataset. -->
-
-{{ curation_rationale_section | default("[More Information Needed]", true)}}
 
 ### Source Data
 
@@ -151,27 +155,6 @@ embeddings from DeepFRI.
 
 {{ source_data_producers_section | default("[More Information Needed]", true)}}
 
-### Annotations [optional]
-
-<!-- If the dataset contains annotations which are not part of the initial data collection, use this section to describe them. -->
-
-#### Annotation process
-
-<!-- This section describes the annotation process such as annotation tools used in the process, the amount of data annotated, annotation guidelines provided to the annotators, interannotator statistics, annotation validation, etc. -->
-
-{{ annotation_process_section | default("[More Information Needed]", true)}}
-
-#### Who are the annotators?
-
-<!-- This section describes the people or systems who created the annotations. -->
-
-{{ who_are_annotators_section | default("[More Information Needed]", true)}}
-
-#### Personal and Sensitive Information
-
-<!-- State whether the dataset contains data that might be considered personal, sensitive, or private (e.g., data that reveals addresses, uniquely identifiable names or aliases, racial or ethnic origins, sexual orientations, religious beliefs, political opinions, financial or health data, etc.). If efforts were made to anonymize the data, describe the anonymization process. -->
-
-{{ personal_and_sensitive_information | default("[More Information Needed]", true)}}
 
 ## Bias, Risks, and Limitations
 
@@ -185,34 +168,26 @@ embeddings from DeepFRI.
 
 {{ bias_recommendations | default("Users should be made aware of the risks, biases and limitations of the dataset. More information needed for further recommendations.", true)}}
 
-## Citation [optional]
+## Citation
 
 <!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
 
 **BibTeX:**
 
-{{ citation_bibtex | default("[More Information Needed]", true)}}
-
-**APA:**
-
-{{ citation_apa | default("[More Information Needed]", true)}}
-
-## Glossary [optional]
-
-<!-- If relevant, include terms and calculations in this section that can help readers understand the dataset or dataset card. -->
-
-{{ glossary | default("[More Information Needed]", true)}}
-
-## More Information [optional]
-
-{{ more_information | default("[More Information Needed]", true)}}
-
-## Dataset Card Authors [optional]
-
-{{ dataset_card_authors | default("[More Information Needed]", true)}}
-
-## Dataset Card Contact
+  @article{KoehlerLeman2023,
+    title = {Sequence-structure-function relationships in the microbial protein universe},
+    volume = {14},
+    ISSN = {2041-1723},
+    url = {http://dx.doi.org/10.1038/s41467-023-37896-w},
+    DOI = {10.1038/s41467-023-37896-w},
+    number = {1},
+    journal = {Nature Communications},
+    publisher = {Springer Science and Business Media LLC},
+    author = {Koehler Leman,  Julia and Szczerbiak,  Pawel and Renfrew,  P. Douglas and Gligorijevic,  Vladimir and Berenberg,  Daniel and Vatanen,  Tommi and Taylor,  Bryn C. and Chandler,  Chris and Janssen,  Stefan and Pataki,  Andras and Carriero,  Nick and Fisk,  Ian and Xavier,  Ramnik J. and Knight,  Rob and Bonneau,  Richard and Kosciolek,  Tomasz},
+    year = {2023},
+    month = apr
+  }
 
-{{ dataset_card_contact | default("[More Information Needed]", true)}}
 
--->
+## Dataset Card Authors
+Matthew O'Meara ([email protected])