| name | ds2pme |
| description | Use when converting PubMed `DocumentSummary` XML into `Pubmed-entry` ASN.1 text, or into the intermediate XML form before final ASN.1 flattening. |
| disable-model-invocation | true |
| user-invocable | true |
ds2pme
Quick Start
- Command:
efetch -db pubmed -id <PMID> -format docsum | ds2pme
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/ds2pme
- Primary modes: default ASN.1 text,
-xml for intermediate XML
When To Use This Tool
- Convert PubMed
DocumentSummary records, rather than full PubmedArticle XML, into Pubmed-entry structures.
- Stay inside a docsum-oriented EDirect workflow when ASN.1 text is the desired downstream format.
- Inspect the intermediate XML before the last flattening step when debugging or archiving conversions.
- Use a lighter-weight alternative to
pma2pme when your upstream source is already docsum output.
Common Patterns
efetch -db pubmed -id 2539356 -format docsum | ds2pme
efetch -db pubmed -id 2539356 -format docsum | ds2pme -xml
efetch -db pubmed -id 2539356 -format docsum | ds2pme -xml |
xtract -pattern Pubmed-entry -element pmid_
Recommended Workflow
- Fetch PubMed records as
-format docsum.
- Use plain
ds2pme when you need final ASN.1 text, or -xml when you want the structured intermediate.
- Confirm that identifiers, title, journal, and article IDs look sensible before storing or reusing the output.
- Switch to
pma2pme instead if your upstream source is full PubmedArticle XML rather than docsum output.
Guardrails
- The wrapper expects PubMed
DocumentSummary XML on stdin, not full PubmedArticle input.
- There is no built-in
--help or --version; unknown arguments fail with Unrecognized argument ....
- Accepted mode switches are
xml/-xml and asn/-asn.
- The default mode emits ASN.1 text beginning with
Pubmed-entry ::= {.
-xml stops before the final xtract -pattern Pubmed-entry -element "." flattening step.- The wrapper depends on EDirect helpers such as
transmute and xtract being on PATH.
