Merge pull request #146 from hubmapconsortium/update-readme

Update README.md

README.md

@@ -1,6 +1,6 @@
 # CCF_tools [![Build Status](https://github.com/obophenotype/CCF_tools/workflows/CI/badge.svg)](https://github.com/obophenotype/CCF_tools/actions?query=workflow%3ACI)
 
-Some simple wrapper code for testing the part/is_a relationships implicit in ASCT-b tables for validity against Uberon and CL and using these to produce OWL via [ROBOT templates](http://robot.obolibrary.org/template).  Two OWL files are produced - one OWL file following OBO standards, and one simple RDF representation with CCF_part_of triples. 
+Some simple wrapper code for testing the part/is_a relationships implicit in ASCT-b tables for validity against Uberon and CL and using these to produce OWL via [ROBOT templates](http://robot.obolibrary.org/template). One OWL file is produced following OBO standards.
 
 
 ![image](https://user-images.githubusercontent.com/112839/95355967-0ecc2380-08be-11eb-85ab-6dea787e43a5.png)
@@ -13,12 +13,10 @@ $ cd src
 $ make all
 ```
 
-### Example output files:
-  - [class_template_Kidney_partonomy.tsv](https://github.com/obophenotype/CCF_tools/blob/master/src/templates/class_template_Kidney_partonomy.tsv)
-  - [ccf_spleen_classes.owl](https://github.com/obophenotype/CCF_tools/blob/master/src/owl/ccf_spleen_classes.owl)
-  - [ind_template_Kidney_partonomy.tsv](https://github.com/obophenotype/CCF_tools/blob/master/src/templates/ind_template_Kidney_partonomy.tsv)
-  - [ccf_spleen_ind.owl](https://github.com/obophenotype/CCF_tools/blob/master/src/owl/ccf_spleen_ind.owl)
-
+### Example output file:
+  - [ccf_Spleen_classes.owl](https://github.com/hubmapconsortium/ccf-validation-tools/blob/master/owl/ccf_Spleen_classes.owl)
+
+
 #### Example heirarchy in OWL (classes)
 ![image](https://user-images.githubusercontent.com/112839/96257807-f1304580-0fb2-11eb-8f94-90ca0891bfc7.png)
 
@@ -29,31 +27,20 @@ $ make all
 ![image](https://user-images.githubusercontent.com/112839/96257915-19b83f80-0fb3-11eb-9c0d-dcd97e50eb4d.png)
 
 
-### [Reports](https://github.com/obophenotype/CCF_tools/blob/master/templates/)
+### Reports
 
+Example report listing not valid relationships
+https://github.com/hubmapconsortium/ccf-validation-tools/blob/master/logs/class_Kidney_log.tsv
 
-Example 
-https://github.com/obophenotype/CCF_tools/blob/master/templates/class_template_Kidney.tsv.log
 
+s | slabel | user_slabel | o | olabel | user_olabel
+-- | -- | -- | -- | -- | --
+  | UBERON:0001284 | renal column | renal column (column of Bertin) | UBERON:0000362 | renal medulla | renal medulla
+  | CL:0000653 | glomerular visceral epithelial cell | glomerular visceral epithelial cell | UBERON:0006852 | glomerular visceral epithelium | glomerular visceral epithelium
 
-s	| slabel	| user_slabel	| o	| olabel	| user_olabel
---|--|--|--|--|--
-UBERON:0001284	| renal column (column of Bertin)	| renal column	| UBERON:0000362	| renal medulla	| renal medulla
-UBERON:0001232	| collecting duct of renal tubule |	Collecting Duct (Medulla) |	UBERON:0001231	 |nephron tubule	| Tubules
+Translation: There is no valid (part_of or is_a) relationship between 'renal column' and 'renal medulla' or between 'glomerular visceral epithelial cell' and 'glomerular visceral epithelium'.  
 
 
-Translation: There is no valid (part_of or is_a) relationship between 'renal column' and 'renal tubule' or between 'collecting duct of renal tubule' and 'renal tubule'.  
-
-
-### Updating tables/adding new ones:
-
-Input tables live in https://github.com/obophenotype/CCF_tools/tree/master/resources/ASCT-b_tables in tsv format.
-
-It is sufficient to copy and paste from originals.
-
-To add a new job, edit the [Makefile](https://github.com/obophenotype/CCF_tools/blob/master/src/Makefile#L3) to add the name of the source file (minus the .tsv file extension) to the JOBS variable:
-
-![image](https://user-images.githubusercontent.com/112839/107493392-743e6280-6b85-11eb-88df-ccbc69214389.png)]