---
title: "Accessing DastaSpace DAASH"
author:
  - Jason Taylor
output: rmarkdown::html_vignette
date: "2026-06-22"
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  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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## Purpose

Within DataSpace, we have a database called the “Database of Annotated Antibody Sequences for HIV-1” or “DAASH”. The purpose of DAASH is to offer users access to antibody sequences, pre-computed germline alignments and related annotations, and predicted structures for a variety of HIV-1 bNAbs (broadly neutralizing antibodies) and mAbs (monoclonal antibodies).

## Data Sources and Processing for DAASH

The nucleotide sequences available in DAASH have been acquired from the Los Alamos National Laboratory (LANL), GenBank, and select publications. These sequences have been run through a processing pipeline which includes applying IgBLAST using the OGRDB germline database and [insert note about where predicted structures come from].

### Accessing DAASH via a `DataSpaceConnection` object

Before getting started with DAASH, please review and follow the instructions in the vignette [Introduction to DataSpaceR](DataSpaceR.html) on how to set up a DataSpace connection object. In particular, as with all DataSpaceR connections, the user must have a DataSpace account set up and have properly configured their netrc file before running the code below.

DAASH data can be obtained from a connection object for one or more mAbs in availableMabs, by passing either an availableMabs object or a DataSpace mab_id to the getDaash() method. In the example below we are getting DAASH data for the VRC01 mAb.


``` r
library(DataSpaceR)

con <- connectDS()

vrc01 <- con$availableMabs[mab_name_std == "VRC01"] |>
  con$getDaash()
```

The getDaash() method can be used to obtain data on a large number of sequences (), but users are advised to restrict their search before calling getDaash() in order to reduce the time required to load the data.

DAASH also stores lineage sequences for some donors, and all available sequences from a given donor can be queried using a donor_id or availableDonors object.


``` r
ch505 <- con$availableDonors[donor_code == "Donor CH505"] |>
  con$getDaash()
#> Presently querying 631 sequences.
```

A DAASH object (obtained via getDaash) has the following fields:

```r
availableStructures
daashMetadata
datasets
donorMetadata
mabMetadata
variableDefinitions
```

Sequences and alignments both can be accessed from the `datasets` field and are loaded automatically.


``` r
ch505$datasets |>
  names()
#> [1] "topCalls"        "alignments"      "sequences"       "alleleSequences" "runInformation"  "pdbAccession"
```

| Dataset           | Description                                                                                                 |
|-------------------|-------------------------------------------------------------------------------------------------------------|
| `sequences`       | BCR neucleotide sequences, CDS mAb IDs, and source information.                                             |
| `alignments`      | Alignment information in an AIRR compatible schema .                                                        |
| `topCalls`        | Top scoring germline alleles in long form.                           |
| `alleleSequences` | Allele sequences for all germlines alleles identified for the antibodies queried form DataSpace.            |
| `runInformation`  | Information regarding the alignment application settings, allele database, and date the alignment was made. |

To access one of these active bindings, call it from the `DataSpaceDaash` object the sequences were loaded to, for example:


``` r
ch505$datasets$topCalls
#> Key: <sequence_id>
#>        sequence_id mab_id     donor_id mab_name_std  donor_code  chain       allele percent_identity matches alignment_length
#>             <char> <char>       <char>       <char>      <char> <char>       <char>            <num>   <int>            <int>
#>    1: cds_seq_1551   <NA> cds_donor_44         <NA> Donor CH505    IGH  IGHD5-24*01          100.000       7                7
#>    2: cds_seq_1551   <NA> cds_donor_44         <NA> Donor CH505    IGH     IGHJ4*02          100.000      46               46
#>    3: cds_seq_1551   <NA> cds_donor_44         <NA> Donor CH505    IGH  IGHV4-59*01           98.276     285              290
#>    4: cds_seq_1551   <NA> cds_donor_44         <NA> Donor CH505    IGH  IGHD3-10*01          100.000       5                5
#>    5: cds_seq_1551   <NA> cds_donor_44         <NA> Donor CH505    IGH     IGHJ5*02          100.000      34               34
#>   ---                                                                                                                        
#> 8399: cds_seq_4036   <NA> cds_donor_44         <NA> Donor CH505    IGH     IGHJ6*02           84.848      28               33
#> 8400: cds_seq_4036   <NA> cds_donor_44         <NA> Donor CH505    IGH IGHV4-59*i03           88.211     217              246
#> 8401: cds_seq_4036   <NA> cds_donor_44         <NA> Donor CH505    IGH  IGHD3-16*02          100.000       5                5
#> 8402: cds_seq_4036   <NA> cds_donor_44         <NA> Donor CH505    IGH     IGHJ2*01           81.818      27               33
#> 8403: cds_seq_4036   <NA> cds_donor_44         <NA> Donor CH505    IGH  IGHV4-61*10           87.698     227              252
#>       score  rank run_application
#>       <num> <int>          <char>
#>    1:  14.1     1         IgBLAST
#>    2:  89.1     1         IgBLAST
#>    3: 438.0     1         IgBLAST
#>    4:  10.3     2         IgBLAST
#>    5:  66.1     2         IgBLAST
#>   ---                            
#> 8399:  35.3     4         IgBLAST
#> 8400: 294.0     4         IgBLAST
#> 8401:  10.3     5         IgBLAST
#> 8402:  29.5     5         IgBLAST
#> 8403: 291.0     5         IgBLAST
```

Descriptions for the various fields in each of these objects can be found using the `variableDefinitions` active binding.


``` r
ch505$variableDefinitions
```

A FASTA file can be exported from a DAASH. By default, sequence headers are generated DataSpace metadata however, the original headers from the sequence source can be used instead by toggling the `orginalHeaders` argument. If no path argument is passed, the function returns the lines of the fasta file instead.


``` r
ch505$getFastaFromSequences(path = "mySequences.fasta")

## or

ch505$getFastaFromSequences(originalHeaders = TRUE, path = "mySequences.fasta")
```

# Accessing DataSpace neutralizing antibody assay data from DAASH

Using the `vrc01` DAASH object created above, we can fetch any available neutralizing antibody data from DataSpace by createing a mAb object and accessing those data from that.


``` r
mabs <- vrc01$availableMabs |>
  con$getMabs()

mabs$datasets |>
  names()
#> [1] "NABMAb"
```