From: An analysis of extensible modelling for functional genomics data
Extension | Support for task: Search |
---|---|
NVT | Different sources will differ in attribute and value, therefore good for local data because NVT can be used to encode arbitrary properties as long as local users are aware of the data types that can be searched. Poor for non-local searches, as inconsistent attributes and values are likely to be used. |
Ontology | Okay if searched with exact matching terms; more difficult to support non-exact match because the search engine is unlikely to search within the ontology structure. |
External file | Not good; there may be no access to the structure of the file. Only information retrieval style requests can be made. |
EMI | Extensions can be searched locally but non-local searches will not be possible unless the extended models are shared. |
Extension | Support for task: Share |
NVT | Good for local sharing, poor for sharing externally because properties may be encoded in NVT in inconsistent ways. |
Ontology | Good if terms agree (if the same ontology has been used). |
External file | Okay if file is in a standard format, otherwise bad (information may be difficult to access). |
EMI | Good for local sharing; cannot be shared externally unless the extended models are shared. |
Extension | Support for task: Read |
NVT | Generally good because writer can be expressive (NVT is better than plain text); only problem is misinterpretation if NVT is used inconsistently. |
Ontology | Good because terms are well defined. |
External file | Good if file is in a standard format, otherwise bad. Other software may be required to access the file, such as for images, archive files, spreadsheets and so on. |
EMI | Good because writer can be as expressive as required. |
Extension | Support for task: Repeat Experiment |
NVT | Okay for local case (especially good if data capture is automated); in general it is a hard problem for the non-local case. |
Ontology | Good for the non-local case. May be less good for local case if local terms are converted to ontology terms and cannot be converted back (ontology may not be able to express all local data in a lossless manner). |
External file | Okay if file is in a standard format, otherwise bad. |
EMI | Good for local case, poor for non-local case unless extensions are widely shared. |
Extension | Support for task: Compare experiments manually |
NVT | Okay, but inconsistencies could be problematic if data types are encoded differently in different settings. |
Ontology | Good because terms are well defined and standard. |
External file | Okay if the file is in a standard format that can be easily processed. |
EMI | Generally good because the model developer can be expressive. |
Extension | Support for task: Compare experiments automatically |
NVT | Good for local case; not good for the non-local case because NVT is likely to have been implemented differently. |
Ontology | Good (consistent representation from different experiments). |
External file | Okay if data are stored in a spreadsheet or tab-delimited text and descriptive metadata are stored correctly within the data format, or if the external file is in a standard format that can be easily processed. |
EMI | Good for local case; cannot be done for the non-local case unless the extensions are widely shared. |
Extension | Support for task: Query |
NVT | Worse than problem for search because queries are generally more precise. |
Ontology | Generally good, but must query more than one language and the software for query evaluation may not be able to call out to a reasoning service (to make use of the ontology structure). |
External file | Not good (it must be assumed that there is no access to structure). |
EMI | Good for local case, cannot be queried non-locally unless the extensions are shared. |
Extension | Support for task: Analyse |
NVT | Not possible; generic analyses must not depend on such data. |
Ontology | May not be relevant; analysis is not usually over ontology terms (but much better than NVT if it is). |
External file | Okay if data are stored in a spreadsheet or tab-delimited text and metadata are stored correctly within the data format, or if the external file is in a standard format that can be easily processed. |
EMI | Okay for local analysis but additional wrappers may be required to allow generic analysis software to access the data. Poor for non-local case as the format will have to be interpreted and software must be written. |
Extension | Support for task: Browse |
NVT | Okay (probably better than plain text). |
Ontology | Good, less chance of misinterpretation than NVT. |
External file | Not good unless file is immediately readable. |
EMI | Good because writer can be expressive. |
Extension | Support for task: Populate |
NVT | Easy to populate but hard to enforce consistency. |
Ontology | Easy as long as ontology is in place and easily accessible. |
External file | Easy to populate but hard to enforce consistency. |
EMI | Easy. |