Merge pull request #4 from Complex-Portal/uniplex-import

Uniplex import

documentation/cp_content.md

@@ -107,14 +107,16 @@ Additional, representative [wwPDB](https://www.ebi.ac.uk/pdbe/) and [EMDB](https
 
 The following [Evidence and Conclusion Ontology (ECO)](http://www.evidenceontology.org/) codes are used to indicate the strength of evidence that a complex exists: 
 
-|ECO Code|Name|Description|
-|--------|----|-----------|
-|ECO:0000353|physical interaction evidence used in manual assertion|Used when experimental evidence for the complexes exists in a single experiment. The complex must be cross-referenced to experimental data in either an IMEx database, wwPDB or EMDB.|
-|ECO:0005543|biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion|Used when experimental evidence for the complexes exists in a single experiment but the constructs are derived from homologous gene products in different species. The complex must be cross-referenced to experimental in either an IMEx database, wwPDB or EMDB.|
-|ECO:0005610|biological system reconstruction evidence based on homology evidence used in manual assertion|Used when experimental evidence exists for a complex in one species and it is desirable to curate a similar complex in another species for which only limited experimental evidence exists. Sequences and number of genome-encoded components are fairly conserved but some divergence may be observed. The complex with the experimental evidence must be annotated with ECO:0000353 or ECO:0005543 and has to be cross-referenced with the qualifier = "inferred-from".|
-|ECO:0005544|biological system reconstruction evidence based on orthology evidence used in manual assertion|Used when experimental evidence exists for a complex in one species (e.g. human) and it is desirable to curate the same complex in another species for which only limited experimental evidence exists (e.g. mouse). Sequences are fairly conserved but some divergence may be observed and the number of genome-encoded components is identical. The complex with the experimental evidence must be annotated with ECO:0000353 or ECO:0005543 and has to be cross-referenced with the qualifier = "inferred-from".|
-|ECO:0005546|biological system reconstruction evidence based on paralogy evidence used in manual assertion|Used when experimental evidence exists for a complex and it is desirable to curate a similar complex in the same species for which only limited experimental evidence exists. Sequences and number of genome-encoded components are fairly conserved but some divergence may be observed. The complex with the experimental evidence must be annotated with ECO:0000353 or ECO:0005543 and has to be cross-referenced with the qualifier = "inferred-from".|
-|ECO:0005547|biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion|Used when no or only partial experimental evidence exists but the complex is generally assumed to exist. Functional studies or ligand binding evidence from pharmacological experiments are often used for the reconstruction of such complexes.|
+|ECO Code|Name|Description|Confidence Score|
+|--------|----|-----------|----------------|
+|[ECO:0000353](http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=ECO:0000353)|physical interaction evidence used in manual assertion|Used when experimental evidence for the complexes exists in a single experiment. The complex must be cross-referenced to experimental data in either an IMEx database, wwPDB or EMDB.|![](https://raw.githubusercontent.com/Complex-Portal/complex-portal-documentation/uniplex-import/assets/score_5_stars.png)|
+|[ECO:0005543](http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=ECO:0005543)|biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion|Used when experimental evidence for the complexes exists in a single experiment but the constructs are derived from homologous gene products in different species. The complex must be cross-referenced to experimental in either an IMEx database, wwPDB or EMDB.|![](https://raw.githubusercontent.com/Complex-Portal/complex-portal-documentation/uniplex-import/assets/score_5_stars.png)|
+|[ECO:0005610](http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=ECO:0005610)|biological system reconstruction evidence based on homology evidence used in manual assertion|Used when experimental evidence exists for a complex in one species and it is desirable to curate a similar complex in another species for which only limited experimental evidence exists. Sequences and number of genome-encoded components are fairly conserved but some divergence may be observed. The complex with the experimental evidence must be annotated with ECO:0000353 or ECO:0005543 and has to be cross-referenced with the qualifier = "inferred-from".|![](https://raw.githubusercontent.com/Complex-Portal/complex-portal-documentation/uniplex-import/assets/score_4_stars.png)|
+|[ECO:0005544](http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=ECO:0005544)|biological system reconstruction evidence based on orthology evidence used in manual assertion|Used when experimental evidence exists for a complex in one species (e.g. human) and it is desirable to curate the same complex in another species for which only limited experimental evidence exists (e.g. mouse). Sequences are fairly conserved but some divergence may be observed and the number of genome-encoded components is identical. The complex with the experimental evidence must be annotated with ECO:0000353 or ECO:0005543 and has to be cross-referenced with the qualifier = "inferred-from".|![](https://raw.githubusercontent.com/Complex-Portal/complex-portal-documentation/uniplex-import/assets/score_4_stars.png)|
+|[ECO:0005546](http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=ECO:0005546)|biological system reconstruction evidence based on paralogy evidence used in manual assertion|Used when experimental evidence exists for a complex and it is desirable to curate a similar complex in the same species for which only limited experimental evidence exists. Sequences and number of genome-encoded components are fairly conserved but some divergence may be observed. The complex with the experimental evidence must be annotated with ECO:0000353 or ECO:0005543 and has to be cross-referenced with the qualifier = "inferred-from".|![](https://raw.githubusercontent.com/Complex-Portal/complex-portal-documentation/uniplex-import/assets/score_4_stars.png)|
+|[ECO:0005547](http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=ECO:0005547)|biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion|Used when no or only partial experimental evidence exists but the complex is generally assumed to exist. Functional studies or ligand binding evidence from pharmacological experiments are often used for the reconstruction of such complexes.|![](https://raw.githubusercontent.com/Complex-Portal/complex-portal-documentation/uniplex-import/assets/score_3_stars.png)|
+|[ECO:0007653](http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=ECO:0007653)|automatically integrated combinatorial computational evidence used in automatic assertion|Used if a complex is predicted to exist from machine-learning data but has no additional supporting evidence.|![](https://raw.githubusercontent.com/Complex-Portal/complex-portal-documentation/uniplex-import/assets/score_2_stars.png)|
+|[ECO:0008004](http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=ECO:0008004)|machine learning method evidence used in automatic assertion|Used if a complex is predicted to exist from machine-learning data and is additionally supported by other evidence such as high confidence covariation data.|![](https://raw.githubusercontent.com/Complex-Portal/complex-portal-documentation/uniplex-import/assets/score_1_star.png)|
 
 ### Retrieval of references for curation evidence