Merge f792dce into 0c893ad

README.md

@@ -24,7 +24,7 @@ pip3 install submit4dn --upgrade
 
 ### Troubleshooting
 
-If you encounter an error containing something like:   
+If you encounter an error containing something like:
 
 ```
  Symbol not found: _PyInt_AsLong
@@ -85,17 +85,17 @@ get_field_info --type Biosample --comments --outfile biosample.xls
 
 Example list of sheets:
 ~~~~
-get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentAgent --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type IndividualMouse --type ExperimentHiC --type ExperimentSetReplicate --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type Image --comments --outfile MetadataSheets.xls
+get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentAgent --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type IndividualMouse --type ExperimentHiC --type ExperimentSetReplicate --type ExperimentCaptureC --type BioFeature --type GenomicRegion --type ExperimentSet --type Image --comments --outfile MetadataSheets.xls
 ~~~~
 
 Example list of sheets: (using python scripts)
 ~~~~
-python3 -m wranglertools.get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentAgent --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type IndividualHuman --type ExperimentHiC --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile MetadataSheets.xls
+python3 -m wranglertools.get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentAgent --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type IndividualHuman --type ExperimentHiC --type ExperimentCaptureC --type BioFeature --type GenomicRegion --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile MetadataSheets.xls
 ~~~~
 
 Example list of sheets: (Experiment seq)
 ~~~~
-python3 -m wranglertools.get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentAgent --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type ExperimentSeq --type Target --type GenomicRegion --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile exp_seq_all.xls
+python3 -m wranglertools.get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentAgent --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type ExperimentSeq --type BioFeature --type GenomicRegion --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile exp_seq_all.xls
 ~~~~
 
 Example list of sheets: (Experiment seq simple)

doc/metadata_submission.md

@@ -69,7 +69,7 @@ In some cases a field value must be formatted in a certain way or the Item will
 In other cases a field value must match a certain pattern. For example, if a field requires a DNA sequence then the submitted value must contain only the characters A, T, G, C or N.
 
 
-_Database Cross Reference (DBxref) fields_, which contain identifiers that refer to external databases, are another case requiring special formatting. In many cases the values of these fields need to be in database\_name:ID format. For example, an SRA experiment identifier would need to be submitted in the form ‘SRA:SRX1234567’ (see also [Basic fields example](#basic-field) above). Note that in a few cases where the field takes only identifiers for one or two specific databases the ID alone can be entered - for example, when entering gene symbols in the *'targeted\_genes’* field of the Target Item you can enter only the gene symbols i.e. PARK2, DLG1.
+_Database Cross Reference (DBxref) fields_, which contain identifiers that refer to external databases, are another case requiring special formatting. In many cases the values of these fields need to be in database\_name:ID format. For example, an SRA experiment identifier would need to be submitted in the form ‘SRA:SRX1234567’ (see also [Basic fields example](#basic-field) above).
 
 ####When a field specifies a linked item
 Some fields in a Sheet for an Item may contain references to another Item. These may be of the same type or different types. Examples of this type of field include the *‘biosource’* field in Biosample or the *‘files’* field in the ExperimentHiC. Note that the latter is also an example of a list field that can take multiple values.
@@ -264,7 +264,24 @@ The scripts accepts the following parameters:.
 
 **To get the complete list of relevant sheets in one workbook:**
 
-    get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type ExperimentRepliseq --type Target --type GenomicRegion --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile AllItems.xls
+    get_field_info --type all --comments --outfile AllItems.xls
+
+
+**You can also generate the sheets needed for a particular type of experiment using pre-set options**
+
+    get_field_info --type hic --comments --outfile HiCMetadata.xls
+
+    Current presets include:
+    - hic for most types of Hi-C eg. in situ, dilution, single cell
+    - chipseq for ChIP-seq
+    - repliseq for 2-phase or multi-phase Repli-seq
+    - atacseq for ATAC-seq
+    - damid for DamID-seq
+    - chiapet for CHIA-Pet and PLAC-seq
+    - capturec for Capture Hi-C
+    - fish for RNA and DNA FISH
+    - spt for Single Particle Tracking Imaging experiments
+
 
 ##<a name="rest"></a>Submission of metadata using the 4DN REST API
 The 4DN-DCIC metadata database can be accessed using a Hypertext-Transfer-Protocol-(HTTP)-based, Representational-state-transfer (RESTful) application programming interface (API) - aka the REST API.  In fact, this API is used by the ```import_data``` script used to submit metadata entered into excel spreadsheets as described [in this document](https://docs.google.com/document/d/1Xh4GxapJxWXCbCaSqKwUd9a2wTiXmfQByzP0P8q5rnE). This API was developed by the [ENCODE][encode] project so if you have experience retrieving data from or submitting data to ENCODE use of the 4DN-DCIC API should be familiar to you.   The REST API can be used both for data submission and data retrieval, typically using scripts written in your language of choice.  Data objects exchanged with the server conform to the standard JavaScript Object Notation (JSON) format.  Libraries written for use with your chosen language are typically used for the network connection, data transfer, and parsing of data  (for example, requests and json, respectively for Python).  For a good introduction to scripting data retrieval (using GET requests) you can refer to [this page](https://www.encodeproject.org/help/rest-api/) on the [ENCODE][encode] web site that also has a good introduction to viewing and understanding JSON formatted data.

doc/schema_info.md

@@ -6,6 +6,7 @@ award.json | Award | award(s)
 biosample.json | Biosample | biosample(s)
 biosample\_cell\_culture.json | BiosampleCellCulture | biosample-cell-cultures, biosample\_cell\_culture
 biosource.json | Biosource | biosource(s)
+bio_feature.json | BioFeature | bio-features, bio\_feature
 construct.json | Construct | construct(s)
 document.json | Document | document(s)
 enzyme.json | Enzyme | enzyme(s)
@@ -19,6 +20,7 @@ file\_fastq.json | FileFastq | files-fastq, file\_fastq
 file\_processed.json | FileProcessed | files-processed, file\_processed
 file\_reference.json | FileReference | files-reference, file\_reference
 file\_set.json | FileSet | file-sets, file\_set
+gene.json | Gene | gene(s)
 genomic\_region.json | GenomicRegion | genomic-regions, genomic\_region
 image.json | Image | image(s)
 individual\_human.json | IndividualHuman | individuals-human, individual\_human
@@ -37,8 +39,7 @@ software.json | Software | software(s)
 sop\_map.json | SopMap | sop-maps, sop\_map
 summary\_statistic.json | SummaryStatistic | summary-statistics, summary\_statistic
 summary\_statistic\_hi\_c.json | SummaryStatisticHiC | summary-statistics-hi-c, summary\_statistic\_hi\_c
-target.json | Target | target(s)
-treatment\_chemical.json | TreatmentChemical | treatments-chemical, treatment\_chemical
+treatment\_agent.json | TreatmentAgent | treatments-agent, treatment\_agent
 treatment\_rnai.json | TreatmentRnai | treatments-rnai, treatment\_rnai
 user.json | User | user(s)
 vendor.json | Vendor | vendor(s)