diff --git a/cami_37.sh b/cami_37.sh
new file mode 100755
index 0000000000000000000000000000000000000000..cf563a89a3a435a476417cf4b9edc6c4a5e58bfc
--- /dev/null
+++ b/cami_37.sh
@@ -0,0 +1,190 @@
+# ====================================================
+# FileName: cami_37.sh
+# Author: Marcos Chow Castro <mctechnology170318@gmail.com>
+# GitHub: https://github.com/mctechnology17
+# Date: 22.11.2021 20:30
+# ====================================================
+
+which conda > /dev/null
+if test $? -ne 0
+then
+ echo "$0: conda is not installed. Please first install it"
+ exit 1
+fi
+
+copyright() {
+cat <<END
+ Copyright (c) 2021 Marcos Chow Castro
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in all
+ copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+END
+ exit 1
+}
+
+usage(){
+cat <<END
+ Usage:
+ sh cami_37.sh
+ OR
+ ./cami_37.sh
+
+ If you can't run the script you have to give it the execution permissions:
+ Try:
+ chmod +x cami_37.sh
+ And finally run:
+ 0) Create cami environment:
+ sh cami_37.sh
+ option: y create cami env
+ 1) Initialize cami:
+ conda activate cami
+ 2) Update cami:
+ sh cami_37.sh
+ option: u update env cami
+ 3) Install cami certificate:
+ sh cami_37.sh
+ option: ce fix drugstone certificates
+ 4) Execute an example:
+ sh cami_37.sh
+ option: ex execute an example
+ 5) Remove tmp file:
+ sh cami_37.sh
+ option: cl remove tmp file
+END
+ exit 1
+}
+
+menu() {
+ echo "===================================="
+ echo "| CAMI ENVIRONMENT INSTALLER |"
+ echo "|----------------------------------|"
+ echo "| h help/usage |"
+ echo "| y create cami env |"
+ echo "| a cami activate |"
+ echo "| u update env cami |"
+ echo "| ce install cami certificate |"
+ echo "| ex execute an example |"
+ echo "| cl remove tmp file |"
+ echo "| d cami deactivate |"
+ echo "| s show env |"
+ echo "| r remove cami env |"
+ echo "| c copyright/permission |"
+ echo "|----------------------------------|"
+ echo "| Press ENTER or CTRL+C to EXIT |"
+ echo "===================================="
+ echo "Continue?"
+}
+
+install_cami() {
+ echo "cami: adding channels"
+ conda config --add channels defaults
+ conda config --add channels conda-forge
+ conda config --add channels bioconda
+ echo "cami: creating environment variable with python 3.7"
+ conda create --name cami -c conda-forge graph-tool python=3.7
+ echo "======================================="
+ echo "| CAMI ENV SUCCESSFULLY CREATED |"
+ echo "|-------------------------------------|"
+ echo "| For a complete installation |"
+ echo "| you must follow the following steps |"
+ echo "| Initialize cami: |"
+ echo "| conda activate cami |"
+ echo "| Update cami: |"
+ echo "| sh cami_37.sh |"
+ echo "| opt: u update env cami |"
+ echo "| Install cami certificate: |"
+ echo "| sh cami_37.sh |"
+ echo "| opt: ce fix drugstone certificate |"
+ echo "|-------------------------------------|"
+}
+
+darwin_certificate() {
+ if [ -d $HOME/opt/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/ ]; then
+ cat drugstone_certificates.txt >> $HOME/opt/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/cacert.pem
+ echo "cami: certificate updated successfully"
+ elif [ -d /opt/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/ ]; then
+ cat drugstone_certificates.txt >> /opt/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/cacert.pem
+ echo "cami: certificate updated successfully"
+ else
+ echo "cami: the directory certifi in cami_env NOT EXIST"
+ fi
+}
+
+linux_certificate() {
+ if [ -d $HOME/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/ ]; then
+ cat drugstone_certificates.txt >> $HOME/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/cacert.pem
+ echo "cami: certificate updated successfully"
+ elif [ -d /anaconda3/envs/cami/lib/python3.7/site-packages/certifi/ ]; then
+ cat drugstone_certificates.txt >> /anaconda3/envs/cami/lib/python3.7/site-packages/certifi/cacert.pem
+ echo "cami: certificate updated successfully"
+ else
+ echo "cami: the directory certifi in cami_env NOT EXIST"
+ fi
+}
+
+install_certificate() {
+case `uname -s` in
+ Darwin) echo "Darwin" && darwin_certificate ;;
+ Linux) echo "Linux" && linux_certificate ;;
+esac
+}
+
+if [ "$1" = "example" ] ; then
+ ./cami/example_run.py
+ exit 0
+elif [ "$1" = "clean" ] ; then
+ rm -r cami/__pycache__
+ rm -r data/tmp
+ exit 0
+fi
+
+remove_cami() {
+ clear
+ echo "|-------------------------|"
+ echo "| Are you sure you want to|"
+ echo "| delete cami env [y/n]?|"
+ echo "+-------------------------+"
+ echo "| Press CTRL+C to exit |"
+ echo "+-------------------------+"
+ read -r cami_del
+ if [ "$cami_del" = "y" ]; then
+ conda env remove -n cami
+ else
+ echo "No change made!"
+ exit 1
+ fi
+}
+
+menu
+read -r cami_tmp
+case $cami_tmp in
+ y|Y) install_cami ;;
+ h|H) usage ;;
+ c|C) copyright ;;
+ a|A) conda activate cami || echo "cami: If it was not activated successfully, please try manually: conda activate cami" ;;
+ u|U) conda env update cami --file=cami_37_env.yaml; pip install domino-python; pip install pcst_fast;pip install requests_html; pip install biodigest ;;
+ d|D) conda deactivate ;;
+ s|S) conda info --envs ;;
+ r|R) remove_cami ;;
+ ce|CE) install_certificate ;;
+ ex|EX) ./cami/example_run.py ;;
+ cl|CL) rm -r cami/__pycache__; rm -r data/tmp ;;
+ *) echo No change made ;;
+esac
+
+# vim: set sw=2 ts=2 sts=2 et ft=sh fdm=indent:
diff --git a/cami_37_env.yaml b/cami_37_env.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..32f5a6dd7b579fb42b37fc9dbc31223cefdd51b4
--- /dev/null
+++ b/cami_37_env.yaml
@@ -0,0 +1,15 @@
+name: cami
+channels:
+ - bioconda
+ - conda-forge
+ - defaults
+dependencies:
+ - python=3.7
+ - graph-tool
+ - networkx
+ - pandas
+ - numpy
+ - jupyter
+ - pip
+ - matplotlib
+ - statsmodels
diff --git a/cami_src/cami.py b/cami_src/cami.py
index 06969d3f99bddb7c1162a5f528448948a76d5434..0ba5922d9ad9e469c36caa91dafbd6292c05bc72 100755
--- a/cami_src/cami.py
+++ b/cami_src/cami.py
@@ -77,7 +77,7 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
if consensus:
cami.reset_cami()
- if evaluate or (not consensus and not evaluate and not seed_variation):
+ if evaluate and (consensus or seed_variation):
cami.make_evaluation()
# SEED VARIATION
@@ -122,7 +122,7 @@ if __name__ == "__main__":
help="List of weights for the tools. If you have [domino, diamond, robust] as list of tools and diamonds weight should be twice as high as the other tools type: 1 2 1")
parser.add_argument('-c', '--consensus', action='store_true', help="run only the consensus prediction part of cami")
parser.add_argument('-var', '--seed_variation', action='store', help="repeat consensus selection multiple times (please provide the number of iterations) while removing 20 percent of the seeds.")
- parser.add_argument('-e', '--evaluate', action='store_true', help="evaluation using DIGEST")
+ parser.add_argument('-e', '--evaluate', action='store_true', help="evaluation using DIGEST", default=False)
parser.add_argument('-o', '--output_dir', action='store', help="path to output directory", default=None)
parser.add_argument('-id', '--identifier', action='store', help="ID for the current excecution of cami. Defaults to a randomly generated ID")
parser.add_argument('-tmp', '--save_temps', action='store_true', help="keep all temporary files")
diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py
index e1ed51adb7f5e0a78e1a1a51a98cf2f14c28bf6f..7b33336e3d1ea95c5a27de999ae676889ae6665d 100644
--- a/cami_src/cami_suite.py
+++ b/cami_src/cami_suite.py
@@ -12,7 +12,6 @@ import matplotlib.pyplot as plt
import itertools
-
def generate_param_combinations(params_dict):
"""
Generates all possible combinations of parameters for the given function(s) and returns them as a list.
@@ -36,6 +35,7 @@ def generate_param_combinations(params_dict):
result.append([function_name, params_str, {'params': param_dict, 'function': function}])
return result
+
def initialize_cami(path_to_ppi_file=''):
cami_params = {}
# find homepath aka ~/cami
@@ -91,8 +91,9 @@ class cami():
consensus approach
"""
- def __init__(self, ppi_graph, seed_lst, tool_wrappers, home_path, initial_seed_lst, uid=None, output_dir='', configuration='camiconf',
- parallelization=False, ncbi=False, debug=False,save_temps=False, toolweights=None):
+ def __init__(self, ppi_graph, seed_lst, tool_wrappers, home_path, initial_seed_lst, uid=None, output_dir='',
+ configuration='camiconf',
+ parallelization=False, ncbi=False, debug=False, save_temps=False, toolweights=None):
"""Instance variables of CAMI
:param ppi_graph: The PPI-Graph on which all predictions in CAMI are based of
@@ -122,7 +123,7 @@ class cami():
self.prediction_tools = [wrapper.name for wrapper in tool_wrappers]
self.toolweights = toolweights
self.home_path = home_path
- if uid==None:
+ if uid == None:
uid = str(uuid.uuid4())
self.uid = str(uid)
if output_dir == None:
@@ -132,7 +133,7 @@ class cami():
if self.debug:
print(f"Output directory of cami: {output_dir}")
self.output_dir = output_dir
-
+
tmp_dir = os.path.join(home_path, 'data', 'tmp', self.uid)
if not os.path.exists(tmp_dir):
os.makedirs(tmp_dir)
@@ -190,7 +191,7 @@ class cami():
tool.set_weight(self.toolweights[tool.code - 1])
else:
tool.set_weight()
-
+
def initialize_all_tools(self):
for tool in self.tool_wrappers:
self.initialize_tool(tool)
@@ -217,7 +218,7 @@ class cami():
seed_gene_lst = [self.ppi_vertex2gene[seed] for seed in self.seed_lst]
ppi_graph_file = os.path.join(self.tmp_dir, f'ppi_graph_{self.uid}.graphml')
self.ppi_graph.save(ppi_graph_file)
-
+
biodigest.setup.main(setup_type="api")
for result_set in self.result_module_sets:
set_validation_results = biodigest.single_validation.single_validation(
@@ -227,7 +228,7 @@ class cami():
distance='jaccard',
ref=set(seed_gene_lst),
ref_id='entrez')
-
+
if set_validation_results['status'] == 'ok':
biodigest.single_validation.save_results(set_validation_results, f'{result_set}_{self.uid}',
self.output_dir)
@@ -238,14 +239,14 @@ class cami():
out_dir=self.output_dir,
prefix=f'{result_set}_{self.uid}',
file_type='png')
-
+
with open(os.path.join(self.tmp_dir, f'{result_set}_{self.uid}_relevance_scores.tsv'), 'w') as f:
rel_score_name = list(set_validation_results['input_values']['values'].keys())[0]
f.write(f'value\t{rel_score_name}\n')
val_res_dct = set_validation_results['input_values']['values'][rel_score_name]
for val in val_res_dct:
f.write(f'{val}\t{val_res_dct[val]}\n')
-
+
# sub_validation_results = biodigest.single_validation.single_validation(
# tar=set(self.result_module_sets[result_set]),
# tar_id='entrez',
@@ -267,7 +268,6 @@ class cami():
# out_dir=self.output_dir,
# prefix=f'{result_set}_{self.uid}',
# file_type='png')
-
def run_threaded_tool(self, tool, pred_sets):
"""run a tool in one thread and save the results into a dictionary pred_sets
@@ -347,7 +347,7 @@ class cami():
# set of all result genes
cami_scores = self.ppi_graph.vertex_properties["cami_score"]
predicted_by = self.ppi_graph.vertex_properties["predicted_by"]
- consens_threshold = min(self.nof_tools, 2)
+ # consens_threshold = min(self.nof_tools, 2)
ppi_graph = self.ppi_graph
seed_list = self.seed_lst
tool_name_map = self.code2toolname
@@ -356,22 +356,22 @@ class cami():
# remove seeds from result sets
for tool in result_sets:
result_sets[tool] -= set(self.seed_lst)
-
+
params_tr = {'hub_penalty': [0.25],
- 'damping_factor': [0.7],
- 'confidence_level': [0.5],
+ 'damping_factor': [0.75],
+ 'confidence_level': [0.8],
'ranking': ['trustrank'],
- 'function': {'cami_v3':cami_v3.run_cami}}
-
+ 'function': {'cami_v3': cami_v3.run_cami}}
+
cami_setting_list = generate_param_combinations(params_tr)
camis = {}
for setting in cami_setting_list:
if setting[1]:
- func_name = setting[0] + '_' +setting[1].rsplit('_', 1)[-1]
+ func_name = setting[0] + '_' + setting[1].rsplit('_', 1)[-1]
else:
func_name = setting[0]
-
+
camis[func_name] = setting[2]
# transform all vertex indices to their corresponding gene names in a result set
@@ -413,7 +413,8 @@ class cami():
sys.setrecursionlimit(recursion_limit)
# save the results in outputfiles
if save_output:
- self.generate_output(cami_method_name, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
+ self.generate_output(cami_method_name, seed_genes, cami_vlist, cami_vertices, putative_vertices,
+ cami_genes,
gene_name_map, codes2tools, cami_scores)
# add seeds to result sets for drugstone and digest
@@ -423,7 +424,6 @@ class cami():
print(
f'With the {len(seed_genes)} seed genes the module predicted by {toolname} contains {len(self.result_module_sets[toolname])} genes')
-
def generate_output(self, cami_method, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
gene_name_map, codes2tools, cami_scores):
# save all predictions by all tools
@@ -468,8 +468,8 @@ class cami():
outputfile.write(f'{gene}\n')
if self.debug:
print(f'saved {tool} output in: {self.output_dir}/{tool}_output_{self.uid}.tsv')
-
- def visualize_and_save_comparison_matrix(self, additional_id='',
+
+ def visualize_and_save_comparison_matrix(self, additional_id='',
title='Intersections of result_gene_sets of all analyzed algorithms.'):
"""Create a comparison matrix of the results of all tools. And save it as png file.
"""
@@ -489,7 +489,7 @@ class cami():
plt.close(comp_fig)
plt.close(norm_fig)
return comp_fig_file, norm_fig_file
-
+
def use_nvenn(self, download=False):
"""Create Venn Diagrams via a external tool named nvenn by degradome.
Sends a request via requests to the degradome server.
@@ -510,7 +510,7 @@ class cami():
else:
print('Cannot use degradome to create venn diagrams of 6 or more tools')
return None
-
+
def download_diagram(self, url):
venn_name = f'{self.output_dir}/vdiagram_{self.uid}'
response = degradome.download_image(url, venn_name + '.png')
diff --git a/cami_src/consensus/cami_v2.py b/cami_src/consensus/cami_v2.py
index 5857bd330c5d2b3d6b5dc818e485b6b5e25780c8..4c27d1637a85a4f496e2ef267117f1d701b90dc6 100644
--- a/cami_src/consensus/cami_v2.py
+++ b/cami_src/consensus/cami_v2.py
@@ -4,12 +4,11 @@ import graph_tool as gt
from utils.networks import trustrank, betweenness, must, closeness
-
# This uses a trustrank algorithm to rank all putative nodes starting from the seeds and only accepts the top 0.X entries
# TODO maybe find a smart way to cutoff automatically?
def run_cami(result_sets, ppi_graph, seed_lst, predicted_by, cami_scores, code2toolname, tool_code, params):
hub_penalty = params['hub_penalty']
- confidence_level = params.get('confidence_level',0.5)
+ confidence_level = params.get('confidence_level', 0.5)
weighted = 'weighted' in params and params['weighted']
ranking_method = params['ranking'] if 'ranking' in params else 'trustrank'
trees = params.get('trees', 5)
@@ -34,6 +33,25 @@ def run_cami(result_sets, ppi_graph, seed_lst, predicted_by, cami_scores, code2t
weights = subnet.new_edge_property("double")
for v, c in counts.items():
weights.a[int(v)] = c
+ # sum = 0
+ # TODO idea for more sophisticated weighting: but then as prior for trustrank and not as weights
+ # for v in subnet.vertices():
+ # c = counts[v]
+ # min_dist = None
+ # for seed in seed_lst:
+ # dist = gt.topology.shortest_distance(ppi_graph, seed, v)
+ # if dist == 2147483647:
+ # dist = 10
+ # if min_dist is None:
+ # min_dist = dist
+ # else:
+ # min_dist = min(min_dist, dist)
+ # min_dist /= len(seed_lst)
+ # score = c + (10-min_dist)
+ # sum += score
+ # weights.a[int(v)] = c
+ # for v in subnet.vertices():
+ # weights.a[int(v)] /= sum
if ranking_method == 'trustrank':
damping_factor = params['damping_factor']
scores = trustrank(subnet, seed_lst, damping_factor, hub_penalty, weights)
@@ -44,8 +62,9 @@ def run_cami(result_sets, ppi_graph, seed_lst, predicted_by, cami_scores, code2t
elif ranking_method == 'harmonic':
scores = closeness(subnet, hub_penalty, weights)
- putative_scores = scores.a[[int(id) for id in putative_vertices]]
+ putative_scores = list(scores.a[[int(id) for id in putative_vertices]])
putative_scores.sort()
+ putative_scores.reverse()
threshold = putative_scores[int(len(putative_vertices) * (1 - confidence_level))]
for v in putative_vertices:
diff --git a/cami_src/consensus/cami_v3.py b/cami_src/consensus/cami_v3.py
index 8326847ed2795851339b9c38804ca74ae29c3321..8e55f108e3855ab964b262e53a7ba5bec02c50e7 100644
--- a/cami_src/consensus/cami_v3.py
+++ b/cami_src/consensus/cami_v3.py
@@ -57,6 +57,7 @@ def run_cami(result_sets, ppi_graph, seed_lst, predicted_by, cami_scores, code2t
pass
putative_scores = list(putative_score_map.values())
putative_scores.sort()
+ putative_scores.reverse()
threshold = putative_scores[int(len(putative_vertices) * (1 - confidence_level))]
for v in putative_vertices:
if putative_score_map[v] >= threshold and putative_score_map[v] > 0:
diff --git a/cami_src/example_run.py b/cami_src/example_run.py
index 386b499259a88e161573ec44ca59527a847c9b28..ab09eacf83f85cd749e6aede8282f52b97537361 100755
--- a/cami_src/example_run.py
+++ b/cami_src/example_run.py
@@ -8,6 +8,7 @@ import subprocess
chdir((sys.argv[0].rsplit('/', 1))[0])
networkfile = "../data/input/networks/example_network.tsv"
seedfile = "../data/input/seeds/example_seeds.txt"
+seedfile = "../data/input/seeds/multiple_sclerosis.tsv"
identifier = "example_run"
-command = f'./cami.py -n {networkfile} -s {seedfile} -id {identifier} -p --f;'
+command = f'./cami.py -n {networkfile} -s {seedfile} -id {identifier} -p -f -v;'
subprocess.call(command, shell=True)
\ No newline at end of file
diff --git a/cami_src/utils/networks.py b/cami_src/utils/networks.py
index e61a812d596abe674c82877550d19b140d6c60e8..131fbdd0a8e438bd5fec5403bb67f3a97fa7046c 100644
--- a/cami_src/utils/networks.py
+++ b/cami_src/utils/networks.py
@@ -10,7 +10,7 @@ import graph_tool.util as gtu
import itertools as it
-def edge_weights(g, base_weigths, hub_penalty, inverse=False):
+def edge_weights(g, base_weigths, hub_penalty = 0, inverse=False):
avdeg = gts.vertex_average(g, "total")[0]
weights = g.new_edge_property("double", val=avdeg)
if base_weigths is not None:
@@ -237,13 +237,15 @@ def must(g, seed_ids, num_trees, hub_penalty, weights=None, tolerance=10):
return score_prop
-def trustrank(g, seed_ids, damping_factor, hub_penalty, weights=None):
+def trustrank(g, seed_ids, damping_factor, hub_penalty=0, weights=None):
if gt.openmp_enabled():
gt.openmp_set_num_threads(6)
- weights = edge_weights(g, weights, hub_penalty, inverse=True)
+ weights = edge_weights(g, weights, hub_penalty, inverse=False)
+
# Call graph-tool to compute TrustRank.
trust = g.new_vertex_property("double")
trust.a[[int(id) for id in seed_ids]] = 1.0 / len(seed_ids)
+
scores = gtc.pagerank(g, damping=damping_factor, pers=trust, weight=weights)
# Compute and return the results.
return scores
diff --git a/data/input/seeds/diabetes_mellitus_type1.list b/data/input/seeds/diabetes_mellitus_type1.list
new file mode 100644
index 0000000000000000000000000000000000000000..f088116efe7cf1245742b7f743b0f3b7a6447124
--- /dev/null
+++ b/data/input/seeds/diabetes_mellitus_type1.list
@@ -0,0 +1,24 @@
+#ID
+entrez.57044
+entrez.326
+entrez.8691
+entrez.3710
+entrez.100303715
+entrez.8245
+entrez.3569
+entrez.3559
+entrez.3630
+entrez.3403
+entrez.3402
+entrez.3407
+entrez.3405
+entrez.3406
+entrez.3414
+entrez.3412
+entrez.3410
+entrez.100271697
+entrez.387082
+entrez.55315
+entrez.6927
+entrez.1493
+entrez.1234
diff --git a/data/input/seeds/diabetes_mellitus_type2.list b/data/input/seeds/diabetes_mellitus_type2.list
new file mode 100644
index 0000000000000000000000000000000000000000..f64ad608548ce3a3ac0368480211b99cd2d1c30c
--- /dev/null
+++ b/data/input/seeds/diabetes_mellitus_type2.list
@@ -0,0 +1,35 @@
+#ID
+entrez.208
+entrez.9479
+entrez.8660
+entrez.169026
+entrez.4813
+entrez.4760
+entrez.4544
+entrez.10644
+entrez.3990
+entrez.3767
+entrez.7466
+entrez.3569
+entrez.3630
+entrez.3667
+entrez.3651
+entrez.3172
+entrez.3159
+entrez.2820
+entrez.2645
+entrez.50982
+entrez.11132
+entrez.6514
+entrez.6833
+entrez.6934
+entrez.6928
+entrez.6927
+entrez.5078
+entrez.5167
+entrez.9882
+entrez.56729
+entrez.5770
+entrez.100188782
+entrez.5468
+entrez.5506
diff --git a/data/input/seeds/hereditary_nephritis.tsv b/data/input/seeds/hereditary_nephritis.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..22e3670d07569a8dd72149e175c48a160cc18074
--- /dev/null
+++ b/data/input/seeds/hereditary_nephritis.tsv
@@ -0,0 +1,53 @@
+#ID Name
+entrez.7076 TIMP1
+entrez.3119 HLA-DQB1
+entrez.7040 TGFB1
+entrez.712 C1QA
+entrez.713 C1QB
+entrez.718 C3
+entrez.3078 CFHR1
+entrez.717 C2
+entrez.10878 CFHR3
+entrez.64231 MS4A6A
+entrez.10855 HPSE
+entrez.29015 SLC43A3
+entrez.3903 LAIR1
+entrez.3075 CFH
+entrez.1670 DEFA5
+entrez.10253 SPRY2
+entrez.8526 DGKE
+entrez.10610 ST6GALNAC2
+entrez.10184 LHFPL2
+entrez.9212 AURKB
+entrez.183 AGT
+entrez.960 CD44
+entrez.7805 LAPTM5
+entrez.56992 KIF15
+entrez.9055 PRC1
+entrez.10461 MERTK
+entrez.2305 FOXM1
+entrez.7157 TP53
+entrez.22909 FAN1
+entrez.64170 CARD9
+entrez.1636 ACE
+entrez.81494 CFHR5
+entrez.335 APOA1
+entrez.4125 MAN2B1
+entrez.10451 VAV3
+entrez.2548 GAA
+entrez.8741 TNFSF13
+entrez.4627 MYH9
+entrez.23603 CORO1C
+entrez.213 ALB
+entrez.101154649 entrez.101154649
+entrez.1880 GPR183
+entrez.3123 HLA-DRB1
+entrez.9332 CD163
+entrez.60498 entrez.60498
+entrez.11326 VSIG4
+entrez.1286 COL4A4
+entrez.5328 PLAU
+entrez.3117 HLA-DQA1
+entrez.1285 COL4A3
+entrez.100653384 entrez.100653384
+entrez.1287 COL4A5
diff --git a/data/input/seeds/retinal_distrophy-inherited.list b/data/input/seeds/retinal_distrophy-inherited.list
new file mode 100644
index 0000000000000000000000000000000000000000..b80da669b97916a20f1621e72bd54332a7e75b07
--- /dev/null
+++ b/data/input/seeds/retinal_distrophy-inherited.list
@@ -0,0 +1,16 @@
+#ID
+entrez.57096
+entrez.23568
+entrez.145226
+entrez.4647
+entrez.10083
+entrez.64072
+entrez.124590
+entrez.25861
+entrez.2527
+entrez.6103
+entrez.6121
+entrez.65217
+entrez.79883
+entrez.5015
+entrez.5631