Description | ||
---|---|---|
Short Name | A short name of the interaction partners | |
Long Name | The name of the interaction partners as given in the literature | |
Additional Information | Information regarding the corresponding interaction partner, which did not fit into any other category. | |
Maintype | Molecule category. We assigned all interaction partners one of the following categories: Protein, DNA, RNA, DNA-Oligonucleotide, RNA-Oligonucleotide, Oligopeptide, Chemical compound, Nanobody, Other. | |
Subtype | The purpose of the subtype category entry is to extend the maintype category. Hence, the interaction partner type is described in more detail. | |
Sequence | DNA or Protein sequence of the corresponding interaction partner. | |
Species | Origin of the corresponding interaction partner | |
Method | Method with which the interaction has been measured | |
Device | Device with which the interaction has been measured | |
Chip | Chip with which the interaction has been measured | |
Software | Software name which has been used to analyse the binding interaction | |
Evaluation | Method which has been applied for the binding kinetic analysis | |
Model | Binding kinetic model which has been applied for the binding kinetic analysis | |
kon | Association rate constant | |
Standard Error kon | Standard error of the association rate constant | |
koff | Dissociation rate constant | |
Standard Error koff | Standard error of the dissociation rate constant | |
KD | Dissociation constant | |
Standard Error KD | Standard error of the dissociation constant | |
Rating 1 | Is raw data present? Y=Yes, N=No, X= Not rated | |
Rating 2 | Is the raw data quality good? Y=Yes, N=No, X=Not rated | |
Rating 3 | Are fits shown? Y=Yes, N=No, X=Not rated | |
Rating 4 | Subjective fit quality. G=Good, B=Bad, R=Reasonable, X=Not rated | |
Comment | Specific comments for the given interaction | |
Position in Article | The positon in the scientific article, where most of the information of the corresponding interaction can be found. | |
Article ID | PMC database ID of the article. | |
Article Title | The full length title od the corresponding article | |
Article Journal | Journal of corresponding article | |
Article DOI | Individual artice identifier | |
Publication Date | Date of publication |
The KOFFI database can also be accessed using our REST-API. It supports complex queries and will return the results in JASON format.
Please send your GET requests to the following URL:
http://koffidb.org/api/interactions/?format=json
Important:
This is a free service from scientists for scientists. Please do not send more than 1 request per three seconds and limit your usage to 100 requests per day. Our computing resources are limited and should be available to everyone! If our API is misused, we will take measures which can lead to permanent blocking. Please also consider downloading the whole database for intense usage.
The returned results from the KOFFI db API will be paginated. Use the “page” parameter to set the page number of the result (e.g. page=2).
page_sizeSpecify the number of search result entries to return on a single page (e.g. page_size=200)
filtersAll queries go in here.
methods__icontains=spr
device__icontains=biacore
(methods__icontains=spr)
(device__icontains=biacore)
(methods__icontains=spr)&(device__icontains=biacore)
%28methods__icontains%3Dspr%29%26%28device__icontains%3Dbiacore%29
http://koffidb.org/api/interactions/?format=json&filters=%28methods__icontains%3Dspr%29%26%28device__icontains%3Dbiacore%29
Search for the protein Thrombin as partner_A or partner_B and show at least 100 entries per page:
Without URL encoding:
http://koffidb.org/api/interactions/?format=json&page_size=100&filters=(partner_A__icontains=thrombin)|(partner_B__icontains=thrombin)
With URL encoding:
http://koffidb.org/api/interactions/?format=json&page_size=100&filters=%28partner_A__icontains%3Dthrombin%29%7C%28partner_B__icontains%3Dthrombin%29
Try it!Search for Thrombin interactions measured with SPR:
Without URL encoding:
http://koffidb.org/api/interactions/?format=json&filters=(partner_A__icontains=thrombin)|(partner_B__icontains=thrombin)%26(method__icontains=spr)
With URL encoding:
http://koffidb.org/api/interactions/?format=json&filters=%28partner_A__icontains%3Dthrombin%29%7C%28partner_B__icontains%3Dthrombin%29%2526%28method__icontains%3Dspr%29
Try it!Search for Thrombin interactions and remove all results measured with SPR:
Without URL encoding:
http://koffidb.org/api/interactions/?format=json&filters=(partner_A__icontains=thrombin)|(partner_B__icontains=thrombin)%26(method__icontains!=spr)
With URL encoding:
http://koffidb.org/api/interactions/?format=json&filters=%28partner_A__icontains%3Dthrombin%29%7C%28partner_B__icontains%3Dthrombin%29%2526%28method__icontains!%3Dspr%29
Try it!Every scientist is welcome to submit interactions for the koffi database. Please follow the following steps: