Project:Curation workflow
Manual annotation steps
- Find descriptions of symbiotic interactions in the literature, see current backlog: Project:New studies to add
- Check if taxon items representing symbiotic interaction partners are already represented in the database (search for taxon names, potential alternative names)
- If not, create taxon items, linking NCBI taxon ID [[Property:P11] if available
- From the item representing host, link to the symbiont with an 'interacts with' Property:P19 statement
- Add the following information about the symbiotic interaction as qualifiers to the 'interacts with' statement. Skip if not known or not specified in the publication.
- Localization of symbiont in host cell/body, Property:P20
- Analytical methods used to identify the symbiont, Property:P22, e.g. light microscopy, metagenome sequencing, phylogenetic marker sequencing
- Analytical methods used to identify the host, Property:P42, e.g. microbiological culture, light microscopy
- Nature/outcome of the interaction, Property:P26 (under development)
- If the interaction is not found in nature but the result of experimental manipulation, use the 'interacts experimentally with' Property:P41 statement instead, with the same qualifiers.
- Cite the source of the information in a reference, using the reference DOI Property:P27 (without the 'doi:' prefix). Reference items will be semi-automatically created/linked later.
- Add information about the environment where the organism was found. For cultured organisms, this should reflect the original environment where the isolate was collected, if known.
- Environmental material of origin Property:P36
- Broad environmental context Property:P38
- Local environmental context Property:P42
- The order in which properties are displayed is set at MediaWiki:Wikibase-SortedProperties; otherwise, statements are displayed in the order they are added.
Automated maintenance tasks
(under development) The following tasks are (semi)-automated, so it is not necessary to do them manually. Scripts are currently run ad-hoc.
- Scripts to create new reference items from DOIs in reference statements and link them
Annotation guidance
NCBI Taxon IDs and representative sequences
(details to come)
Subject body part (P20)
Terms should be drawn from the Gene Ontology or Uberon.
Environment terms (P36, P38, P40)
Follow the guidelines for using EnvO terms in the MIxS standard: https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5
Use subclasses/instances of the following classes with the respective properties. The items within each class should be mapped to subclasses/instances of the corresponding EnvO terms.
| Property | Class | EnvO term |
|---|---|---|
| Property:P36 environmental material of origin | Item:Q1597 environmental material | http://purl.obolibrary.org/obo/ENVO_00010483 |
| Property:P38 environmental system of origin | Item:Q1602 environmental system | http://purl.obolibrary.org/obo/ENVO_01000254 |
| Property:P40 local environmental context | Item:Q1673 astronomical body part | http://purl.obolibrary.org/obo/ENVO_01000813 |
References without DOIs
If a publication does not have a DOI, a reference item has to be created and linked manually. If the full text is available online, specify the URL Property:P15, otherwise give the citation as free text Property:P14.