Searching model
Models can be accessed by browsing through the list of your models which you can access to, or via the search facility.
BioModels Search Web Interface
What can you search for?
Users can search for models using the search box located on the top right of every page, as well as next to the search results on the search page. Models can be searched in terms of name, description, the person submitter, the format, the version of the format, and the publication information. For more complex queries, we recommend you consult BioModels Search syntax.
Search results page
The search results can be ordered (by choosing sorting criteria in the drop down box on the top of results list) in terms of author name, perennial identifier, name and publication year. If not choosing, the default order of results is based on their relevance, i.e. the proximity of the terms in the models.
The search query is embedded in the URL shown in the browser, which enables users to bookmark search results. More information about the models appearing in the search results can be accessed by clicking on name of the model.
Search results are influenced by the models to which a user has access to. As such, searches performed without signing in will only cover the public models.
Facets
Vertical faceted menus, if available, are displayed on the left side of the search results page. You can narrow your search results by ticking in checkboxes embedded for every facet or typing keywords into the searching text boxes on the top of every faceted category.
Search syntax
Overview
- Use quotes to search for a specific phrase: (e.g. a search for "MAPK cascade" would not include a model containing ther term "cascade" on its own.).
- Search terms can be combined using AND, OR, NOT: (e.g. "lung cancer" AND NOT "homo sapiens")
- It is possible to restrict the search to specific fields: (e.g. curationstatus:"Manually curated" AND disease:"Cancer").
In the table below, a brief overview of some useful query syntax basics is presented.
| Element | Meaning | Usage | Example | Description |
|---|---|---|---|---|
| AND | In addition to | term 1 AND term 2 | "MAPK cascade" AND cancer | Matches models where both MAPK cascade and cancer occur. |
| OR | Equivalence | term 1 OR term 2 | "MAPK cascade" OR "lung cancer" | Matches models where either MAPK cascade or lung cancer |
| NOT | Exclusion | term 1 NOT term 2 | coding NOT fragment | Matches models containing coding but not fragment |
| * | Wildcard | partialTerm* | mapk* | Matches models for instance mapk, mapks, mapk2, or mapkinase. |
| " " | Exact match | "search term" | "homo sapiens" | Exact matching for models containing the whole phrase homo sapiens |
| ( ) | Grouping | (search term) | (mapk OR mapk3) AND ERK | Matches models containing either mapk3 or mapk AND ERK |
| Field: | Field-specific search | fieldId:term | description:dopamine | Matches for a field description containing dopamine. |
To use characters that have a special meaning in the query syntax literally in your query, you must escape them with a backslash in order to be correctly interpreted, e.g. use name:\(EGFR overexpression\) to search for the model name containing (EGFR overexpression). The current list of special characters is:
+ - && || ! ( ) { } [ ] ^ " ~ \* ? : \\ BioModels query fields
Supported query fields for searching specific models in BioModels. The following table shows syntax of based-field queries that BioModels is supporting.
| Field | Example | Description |
|---|---|---|
| curationstatus | curationstatus:"Manually curated" | Lists all manually curated models. Notes: The alternative is Non-curated. |
| modelformat | modelformat:"SBML" | Matches all models which format is SBML. Notes: The alternatives could be Orignial code, MATLAB (Octave), etc. |
| modellingapproach | modellingapproach:"Ordinary differential equation model" | Matches all models which modelling approach is Ordinary differential equation model. Notes: The other modelling approaches are Constraint-based model, Logical model, Petri net. |
| modelflag | modelflag:"Non Miriam" | Matches all models not compatible with Miriam. Notes: We support the other model flags such as Non Kinetic, Non Miriam, Sbml Extended. |
| TAXONOMY | TAXONOMY:9606 | Matches all models containing at least one model element that is annotated with TAXONOMY:9606 (i.e. homo sapiens). |
| disease | disease:"Down Syndrome" | Matches all models containing at least one model element which is annotated with the disease name Down Syndrome in Human Disease Ontology (i.e. DOID:14250). |
| GO | GO:GO:0016049 | Matches all models having model elements that were annotated with Gene Ontology term cell growth. |
| UNIPROT | UNIPROT:P30084 | Matches all models having model elements that were annotated with UniProt term Enoyl-CoA hydratas, mitochondrial. |
| CHEBI | CHEBI:CHEBI:15343 | Matches all models having model elements that were annotated with ChEBI accession CHEBI:15343. |
| ENSEMBL | ENSEMBL:ENSG00000111640 | Matches all models having model elements that were annotated with Ensembl term GAPDH. |
| name | name:"Diabetes" | Matches all models which name contains the word Diabetes. |
| description | description:"Parkinson" | Matches all models which description contains the word Parkinson. |
| submitter | submitter:"Sheriff" | Matches all models which the submitter's name contains the word Sheriff. |
| PUBMED | PUBMED:"27869123" | Matches all models which the publication is associated PUBMED entry identified by 27869123. |
| publication_authors | publication_authors:"Dalle Pezze" | Matches all models which Dalle Pezze is one of its authors. |
| pubmed_title | pubmed_title:"Ultrasensitivity in the mitogen-activated protein kinase cascade" | Matches all models which the publication title is Ultrasensitivity in the mitogen-activated protein kinase cascade. |
To know more about the fields that are being supported query fields, please visit About BioModels's Metadata. On this page, the fields which values are true on Searchable column can be searched.
Share research results
To share the specific search results, copy the url where the search terms are embedded. For example: you can share the following link
https://www.ebi.ac.uk/biomodels/search?query=MAPK+cascade+AND+curationstatus%3A%22Manually+curated%22&numResults=10
to search for
MAPK cascade AND curationstatus:"Manually curated"
Download search results
On the search page, you are allowed to download either a single result or a bulk of models. By ticking the checkboxes on the right side of each row in the result page, you have selected the models interest. You may click Select all link to select all the models showing on the current page. The number of models showing on the page can be changed by using the pagination. In the time being, BioModels supports download multiple models but limits 100 models at once.