Add landscape analysis (#17)

This PR adds an workflow for automating the analysis of the landscape of
a given domain, given a (mostly declarative) configuration describing
the resources in that domain. It includes five landscape analyses:

1.
[Disease](https://github.com/biopragmatics/semra/blob/disease-landscape/scripts/disease/disease-landscape.ipynb)
2. [Cell & Cell
Line](https://github.com/biopragmatics/semra/blob/disease-landscape/scripts/cell/cell-landscape.ipynb)
3.
[Anatomy](https://github.com/biopragmatics/semra/blob/disease-landscape/scripts/anatomy/anatomy-landscape.ipynb)
4. [Protein
Complex](https://github.com/biopragmatics/semra/blob/disease-landscape/scripts/complex/complex-landscape.ipynb)
5.
[Gene](https://github.com/biopragmatics/semra/blob/disease-landscape/scripts/gene/gene-landscape.ipynb)

To do:

- [x] Make comparison chart between raw mappings + processed
- [x] Integrate GARD
- [x] Integrate OMIM
- [x] Integrate Orphanet
- [x] Remove HPO
- [x] Create upset plot
- [x] Slice out irrelevant hierarchies from MeSH, EFO, etc.
- [x] Create landscape histogram

This PR also makes other improvements to the underlying SeMRA pipeline
and web app, including closes #16.



![](https://raw.githubusercontent.com/biopragmatics/semra/disease-landscape/notebooks/landscape/disease/graph.svg)

We're able to automatically generate an UpSet plot like the one in [How
many rare diseases are there? (Haendel *et al.*,
2020)](https://doi.org/10.1038/d41573-019-00180-y) (a similar plot to
the following appears in the [supplementary
info](https://media.nature.com/original/magazine-assets/d41573-019-00180-y/17308594)
and an explanation appears on
[zenodo](https://zenodo.org/records/3478576)). Note that our plot is
about all diseases, not specifically rare ones:


![](https://raw.githubusercontent.com/biopragmatics/semra/disease-landscape/notebooks/landscape/disease/landscape_upset.svg)

The following histogram estimates how many diseases there are.
Importantly, it shows how many show up in a single resource, how many
show up in all resources, and how many show up in a few


![](https://raw.githubusercontent.com/biopragmatics/semra/disease-landscape/notebooks/landscape/disease/landscape_histogram.svg)

.gitignore

@@ -901,3 +901,4 @@ FodyWeavers.xsd
 scratch/
 *.jnl
 *.jar
+scripts/Untitled.ipynb

notebooks/landscape/README.md

@@ -0,0 +1,41 @@
+# Landscape Analysis
+
+This folder contains results from a workflow for automating the analysis of the landscape of a given domain,
+given a declarative configuration describing the resources in that domain. It includes five landscape analyses:
+
+1. [Disease](disease/disease-landscape.ipynb)
+2. [Cell & Cell Line](cell/cell-landscape.ipynb)
+3. [Anatomy](anatomy/anatomy-landscape.ipynb)
+4. [Protein Complex](complex/complex-landscape.ipynb)
+5. [Gene](gene/gene-landscape.ipynb)
+
+## Example
+
+Below, we highlight the disease landscape. Each analysis creates a graph of the processed mappings.
+
+![](disease/graph.svg)
+
+We're able to automatically generate an UpSet plot like the one in [How many rare diseases are there? (Haendel *et
+al.*, 2020)](https://doi.org/10.1038/d41573-019-00180-y)  (a similar plot to the following appears in
+the [supplementary info](https://media.nature.com/original/magazine-assets/d41573-019-00180-y/17308594) and an
+explanation appears on [zenodo](https://zenodo.org/records/3478576)). Note that our plot is about all diseases, not
+specifically rare ones:
+
+![](disease/landscape_upset.svg)
+
+The following histogram estimates how many diseases there are. Importantly, it shows how many show up in a single
+resource, how many show up in all resources, and how many show up in a few
+
+![](disease/landscape_histogram.svg)
+
+## Summary
+
+A summary chart over all landscapes can be generated with `landscape.py`.
+
+| name    | raw_term_count | unique_term_count | reduction |
+|---------|---------------:|------------------:|----------:|
+| disease |         410173 |            243730 |  0.405787 |
+| anatomy |          37917 |             32108 |  0.153203 |
+| complex |          15869 |              7775 |  0.510051 |
+| gene    |    4.94578e+07 |       4.87886e+07 |  0.013529 |
+| cell    |         207019 |            166274 |  0.196818 |