From 8b95238213e0ba01d25df765f3df18d2d45fd076 Mon Sep 17 00:00:00 2001 From: bhushankhope <53601863+bhushankhope@users.noreply.github.com> Date: Mon, 27 Jun 2022 14:01:55 -0400 Subject: [PATCH] Update README.md and clean up (#13) * added changelog.md * updated readme.md * Update README.md * Update README.md Co-authored-by: Bruce W. Herr II --- CHANGELOG.md | 58 +++++++ README.md | 88 ++-------- demo-input.txt => sampledata/demo-input.txt | 66 ++++---- demo-input.xlsx => sampledata/demo-input.xlsx | Bin sampledata/demo-output.csv | 20 +++ .../demo-output.tree.txt | 0 demo-output.xls => sampledata/demo-output.xls | 0 .../demo-output.xls.dot | 0 sampledata/placenta-input.tsv | 153 ++++++++++++++++++ sampledata/placenta-output.csv | 64 ++++++++ 10 files changed, 340 insertions(+), 109 deletions(-) create mode 100644 CHANGELOG.md rename demo-input.txt => sampledata/demo-input.txt (97%) rename demo-input.xlsx => sampledata/demo-input.xlsx (100%) create mode 100644 sampledata/demo-output.csv rename demo-output.tree.txt => sampledata/demo-output.tree.txt (100%) rename demo-output.xls => sampledata/demo-output.xls (100%) rename demo-output.xls.dot => sampledata/demo-output.xls.dot (100%) create mode 100644 sampledata/placenta-input.tsv create mode 100644 sampledata/placenta-output.csv diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..e98606e --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,58 @@ +# Changelog + +Changelog for the ASCT+B Generator + +## 1.1.0 - 2022-06-25 + +* Added a feature to generate CSV files from TSV/CSV files. +* Added typings and docstrings. +* Modified the code according to PEP-8 style guide. + +## 1.0.3 - 2022-05-25 + +### Added in 1.0.3 + +* Fixed a bug causing each reference to incorrectly span 5 columns. References now correctly span 3 columns. + +## 1.0.2 - 2022-02-20 + +### Added in 1.0.2 + +* Added "note" and "ABBR" (abbreviation) fields for each feature. These columns are now required in the input file. +* The first 10 lines of the input file are now assumed to contain a descriptive header. This is duplicated to the output file. The 11th line in the input file is assumed to be a per-column header that is ignored. + +## 1.0.1 - 2022-02-15: + +### Added in 1.0.1 + +* Test to be sure entities (anatomical structures, cell types, biomarkers and references) don't have commas in their names. +* Added a command line argument users can set to force anatomical structures to be unique (ie., each has one and only one parent). When set, if the same sub-structure exists in multiple parent-structures, then each child structure would need to be uniquely named. By default, a child structure can have multiple parent structures. +* Added a command line argument users can set to cause the program to automatically create missing features, when features are used. For example, if a biomarker is assigned to a cell type, by default, the biomarker must be independently defined but now users can optionally disable this requirement. Anatomical structures must always be defined. + +## 1.0 - 2022-02-14 + +### Added in 1.0 + +* Removed the (erroneous) assumption that an anatomical structure can only have a single parent, added more validation of the inputs, added debugging output options, and better handle command line arguments. Also various bug fixes. +* These are the significant differences from version v0.1 and v1.0. + + 1. The command line arguments have been greatly simplified. + 2. The number of AS levels is automatically computed. + 3. The input file has changed with this release. Cells are listed in a separate column from the children column. + 4. Biomarkers and references can now be added to any anatomical structure. + 5. The anytree Python module is required. + 6. A header is autogenerate in the output file. + 7. A DOT file can be generated to display the tree in Graphviz. + 8. Lots of tests to validate the input file + +## 1.0-beta - 2022-02-11 + +### Added in 1.0-beta + +* This is a complete rewrite of the program. This version has none of the limitations from the alpha version, it includes more data validation, and requires less user intervention. + +## 0.1-alpha - 2022-02-02 + +### Added in 0.1-alpha + +* This is a proof of concept and not meant for production use. \ No newline at end of file diff --git a/README.md b/README.md index 317a089..caa9dd0 100644 --- a/README.md +++ b/README.md @@ -1,43 +1,16 @@ # ASCT+B Generator -This program converts a simple TSV file into a HuBMAP ASCT+B table. +This program converts a simple CSV file into a HuBMAP CCF ASCT+B table. -The included file "demo-input.txt" was generated by Excel using the "demo-input.xlsx" file (Save As "Tab delimited Text"). The generated output is a TSV file. The example file "demo-output.xls" was generated by the program. +In the sampledata directory, an included file "demo-input.txt" was generated by Excel using the "demo-input.xlsx" file (Save As "Tab delimited Text"). The generated output is a CSV file. The example file "demo-output.csv" was generated by the program. -## Version +## Change Log -May 25, 2022 +See the [ChangeLog](CHANGELOG.md) for the latest developments. -- Fixed a bug causing each reference to incorrectly span 5 columns. References now correctly span 3 columns. +## Known Issues -Feb 20, 2022 - -- Added "note" and "ABBR" (abbreviation) fields for each feature. These columns are now required in the input file. -- The first 10 lines of the input file are now assumed to contain a descriptive header. This is duplicated to the output file. The 11th line in the input file is assumed to be a per-column header that is ignored. - -Feb 15, 2022: - -- Test to be sure entities (anatomical structures, cell types, biomarkers and references) don't have commas in their names. - -- Added a command line argument users can set to force anatomical structures to be unique (ie., each has one and only one parent). When set, if the same sub-structure exists in multiple parent-structures, then each child structure would need to be uniquely named. By default, a child structure can have multiple parent structures. -- Added a command line argument users can set to cause the program to automatically create missing features, when features are used. For example, if a biomarker is assigned to a cell type, by default, the biomarker must be independently defined but now users can optionally disable this requirement. Anatomical structures must always be defined. - -**v1.0** - Feb 14, 2022: Removed the (erroneous) assumption that an anatomical structure can only have a single parent, added more validation of the inputs, added debugging output options, and better handle command line arguments. Also various bug fixes. - -These are the significant differences from version v0.1 and v1.0. - - 1. The command line arguments have been greatly simplified. - 2. The number of AS levels is automatically computed. - 3. The input file has changed with this release. Cells are listed in a separate column from the children column. - 4. Biomarkers and references can now be added to any anatomical structure. - 5. The anytree Python module is required. - 6. A header is autogenerate in the output file. - 7. A DOT file can be generated to display the tree in Graphviz. - 8. Lots of tests to validate the input file - -**v1.0-beta** - Feb 11, 2022: This is a complete rewrite of the program. This version has none of the limitations from the alpha version, it includes more data validation, and requires less user intervention. - -**v0.1-alpha** - Feb 2, 2022: This is a proof of concept and not meant for production use. +See the [Issue Tracker](https://github.com/hubmapconsortium/asct-b-generator/issues?q=is%3Aissue+is%3Aopen+label%3A%22known+issue%22) for known issues. ## Assumptions @@ -81,7 +54,7 @@ Generate ASCT+B table. positional arguments: input Input file - output Output file (TSV) + output Output file (CSV) optional arguments: -h, --help show this help message and exit @@ -91,20 +64,20 @@ optional arguments: -v, --verbose Print the tree to the terminal. ``` -To process the demo input file and generate a TSV file that can be opened by Excel +To process the demo input file and generate a CSV file that can be opened by Excel ``` -process.py +process.py ``` ``` -process.py demo-input.txt demo-output.xls +process.py demo-input.txt demo-output.csv ``` -## Input file (TSV) +## Input file (CSV) -The tab delimited file must contain a header line and the following twelve columns: +The comma delimited file (tab separated is also supported) must contain a header line and the following twelve columns: NAME (REF DOI) LABEL (REF DETAILS) ID (REF NOTES) NOTE ABBR TYPE CHILDREN CELLS GENES PROTEINS PROTEOFORMS LIPIDS METABOLITES FTUs REFERENCES @@ -138,40 +111,3 @@ E-cadherin Protein doi:10.1093/oxfordjournals.humrep.a136365 PMID: 3558758 Reference McKay et al 1961 McKay, D., Pinkerton, J., Hertig, A. & Danziger, S. (1961). The Adult Human Ovary: A Histochemical Study. Obstetrics & Gynecology, 18(1), 13-39. Reference ``` - -## Known problems and limitations - -1. The program should validate the biomarkers using the TYPE field designation. - -1. Export ASCT+B table as CSV file. - -1. Need to allow for case-independence. At present if a cell type is defined with upper cases and applied to a structure in lower case then the program will consider these different entities and throw an error. - -1. Need better example and docs. - -1. The program should allow for non-unique "author preferred name" field values. - -1. Test if a parent has a child which is actually the parent. - -1. Need to strip blank space for the left/right of each text field. - -1. If there are dulicate references in a comma separated list of references (column 15) this causes an error claiming a feature hasn't been defined when actually the error is about duplications in the comma separated list of features. The program needs to test for duplications in feature lists. - -1. The program requires UTF-8 encoding. - -1. There is a bug in Excel where by when generating TSV or CSV files, it may incorrectly include a lot of empty COLUMNS. For example, if the input file only has 15 columns of data, Excel may generate a TSV or CSV file that includes 30 columns that correctly includes the 15 columns of data and another 15 empty columns. This causes the program to error. The program needs to include a workaround for this issue. - - ``` - ERROR: incorrect number of fields in line. The tab-delimited line should contain the following 15 fields: - name, label, ID, node, abbreviation, feature type, children, cells, genes, proteins, proteoforms, lipids, metabolites, FTU, references - Number of fields found in line: - ``` - -1. There is a bug in Excel where by when generating TSV or CSV files, it may incorrectly include a lot of empty ROWS. For example, if the input file only has 100 rows of data, Excel may generate a TSV or CSV file that includes 500 rows that correctly includes the 100 rows of data and another 400 empty rows. This causes the program to error. The program needs to include a workaround for this issue. - - ``` - ERROR: all features must have a unique name. - [ type:] - [ type:] - ``` - diff --git a/demo-input.txt b/sampledata/demo-input.txt similarity index 97% rename from demo-input.txt rename to sampledata/demo-input.txt index 0c6dcb2..3d1e3de 100644 --- a/demo-input.txt +++ b/sampledata/demo-input.txt @@ -1,33 +1,33 @@ -"Anatomical Structures, Cell Types and Biomarkers Table for " - -Author Name(s): -Author ORCID(s): -Reviewer(s): -Reviewer ORCID(s): -General Publication(s): -Data DOI: Will be added after table is finalized and published -Date: 4/1/22 -Version Number: v -NAME (REF DOI) LABEL (REF DETAILS) ID (REF NOTES) NOTES ABBR TYPE CHILDREN CELLS GENES PROTEINS PROTEOFORMS LIPIDS METABOLITES FTUs REFERENCES (DOI) -organ UBERON:1234 AS "sub struct 1, sub struct 2" -sub struct 1 UBERON:0001 AS "sub struct 3, sub struct 4" -sub struct 2 UBERON:0002 AS "sub struct 5, sub struct 6" -sub struct 3 as-3 UBERON:0003 AS "cell1,cell2,cell3" -sub struct 4 as-4 UBERON:0004 AS "cell1,cell2" -sub struct 5 as-5 UBERON:0005 AS "cell1,cell2,cell3" -sub struct 6 as-6 UBERON:0006 AS cell3 -cell1 c1 CT gene1 "protein1,protein2" lipid1 metabolite1 ref1 -cell2 c2 CT "gene1,gene2,gene3" "proteo1, proteo2" lipid2 ref2 -cell3 c3 CT "gene1,gene3" protein2 proteo2 metabolite1 "ref1,ref2" -gene1 Gene -gene2 Gene -gene3 Gene -protein1 Protein -protein2 Protein -proteo1 Proteoform -proteo2 Proteoform -lipid1 Lipid -lipid2 Lipid -metabolite1 Metabolite -ref1 Reference -ref2 Reference +"Anatomical Structures, Cell Types and Biomarkers Table for " + +Author Name(s): +Author ORCID(s): +Reviewer(s): +Reviewer ORCID(s): +General Publication(s): +Data DOI: Will be added after table is finalized and published +Date: 4/1/22 +Version Number: v +NAME (REF DOI) LABEL (REF DETAILS) ID (REF NOTES) NOTES ABBR TYPE CHILDREN CELLS GENES PROTEINS PROTEOFORMS LIPIDS METABOLITES FTUs REFERENCES (DOI) +organ UBERON:1234 AS "sub struct 1, sub struct 2" +sub struct 1 UBERON:0001 AS "sub struct 3, sub struct 4" +sub struct 2 UBERON:0002 AS "sub struct 5, sub struct 6" +sub struct 3 as-3 UBERON:0003 AS "cell1,cell2,cell3" +sub struct 4 as-4 UBERON:0004 AS "cell1,cell2" +sub struct 5 as-5 UBERON:0005 AS "cell1,cell2,cell3" +sub struct 6 as-6 UBERON:0006 AS cell3 +cell1 c1 CT gene1 "protein1,protein2" lipid1 metabolite1 ref1 +cell2 c2 CT "gene1,gene2,gene3" "proteo1, proteo2" lipid2 ref2 +cell3 c3 CT "gene1,gene3" protein2 proteo2 metabolite1 "ref1,ref2" +gene1 Gene +gene2 Gene +gene3 Gene +protein1 Protein +protein2 Protein +proteo1 Proteoform +proteo2 Proteoform +lipid1 Lipid +lipid2 Lipid +metabolite1 Metabolite +ref1 Reference +ref2 Reference diff --git a/demo-input.xlsx b/sampledata/demo-input.xlsx similarity index 100% rename from demo-input.xlsx rename to sampledata/demo-input.xlsx diff --git a/sampledata/demo-output.csv b/sampledata/demo-output.csv new file mode 100644 index 0000000..01b2c28 --- /dev/null +++ b/sampledata/demo-output.csv @@ -0,0 +1,20 @@ +"Anatomical Structures, Cell Types and Biomarkers Table for ",,,,,,,,,,,,,, +,,,,,,,,,,,,,, +Author Name(s):,,,,,,,,,,,,,, +Author ORCID(s):,,,,,,,,,,,,,, +Reviewer(s):,,,,,,,,,,,,,, +Reviewer ORCID(s):,,,,,,,,,,,,,, +General Publication(s):,,,,,,,,,,,,,, +Data DOI:,Will be added after table is finalized and published,,,,,,,,,,,,, +Date:,4/1/22,,,,,,,,,,,,, +Version Number:,v,,,,,,,,,,,,, +AS/1,AS/1/LABEL,AS/1/ID,AS/1/NOTE,AS/1/ABBR,AS/2,AS/2/LABEL,AS/2/ID,AS/2/NOTE,AS/2/ABBR,AS/3,AS/3/LABEL,AS/3/ID,AS/3/NOTE,AS/3/ABBR,CT/1,CT/1/LABEL,CT/1/ID,CT/1/NOTE,CT/1/ABBR,BGene/1,BGene/1/LABEL,BGene/1/ID,BGene/1/NOTE,BGene/1/ABBR,BGene/2,BGene/2/LABEL,BGene/2/ID,BGene/2/NOTE,BGene/2/ABBR,BGene/3,BGene/3/LABEL,BGene/3/ID,BGene/3/NOTE,BGene/3/ABBR,BProtein/1,BProtein/1/LABEL,BProtein/1/ID,BProtein/1/NOTE,BProtein/1/ABBR,BProtein/2,BProtein/2/LABEL,BProtein/2/ID,BProtein/2/NOTE,BProtein/2/ABBR,BProteoform/1,BProteoform/1/LABEL,BProteoform/1/ID,BProteoform/1/NOTE,BProteoform/1/ABBR,BProteoform/2,BProteoform/2/LABEL,BProteoform/2/ID,BProteoform/2/NOTE,BProteoform/2/ABBR,BLipid/1,BLipid/1/LABEL,BLipid/1/ID,BLipid/1/NOTE,BLipid/1/ABBR,BMetabolites/1,BMetabolites/1/LABEL,BMetabolites/1/ID,BMetabolites/1/NOTE,BMetabolites/1/ABBR,REF/1,REF/1/DOI,REF/1/NOTES,REF/2,REF/2/DOI,REF/2/NOTES +organ,,UBERON:1234,,,sub struct 1,,UBERON:0001,,,sub struct 3,as-3,UBERON:0003,,,cell1,c1,,,,gene1,,,,,,,,,,,,,,,protein1,,,,,protein2,,,,,,,,,,,,,,,lipid1,,,,,metabolite1,,,,,ref1,,,,,,, +organ,,UBERON:1234,,,sub struct 1,,UBERON:0001,,,sub struct 3,as-3,UBERON:0003,,,cell2,c2,,,,gene1,,,,,gene2,,,,,gene3,,,,,,,,,,,,,,,proteo1,,,,,proteo2,,,,,lipid2,,,,,,,,,,ref2,,,,,,, +organ,,UBERON:1234,,,sub struct 1,,UBERON:0001,,,sub struct 3,as-3,UBERON:0003,,,cell3,c3,,,,gene1,,,,,gene3,,,,,,,,,,protein2,,,,,,,,,,proteo2,,,,,,,,,,,,,,,metabolite1,,,,,ref1,,,ref2,, +organ,,UBERON:1234,,,sub struct 1,,UBERON:0001,,,sub struct 4,as-4,UBERON:0004,,,cell1,c1,,,,gene1,,,,,,,,,,,,,,,protein1,,,,,protein2,,,,,,,,,,,,,,,lipid1,,,,,metabolite1,,,,,ref1,,,,,,, +organ,,UBERON:1234,,,sub struct 1,,UBERON:0001,,,sub struct 4,as-4,UBERON:0004,,,cell2,c2,,,,gene1,,,,,gene2,,,,,gene3,,,,,,,,,,,,,,,proteo1,,,,,proteo2,,,,,lipid2,,,,,,,,,,ref2,,,,,,, +organ,,UBERON:1234,,,sub struct 2,,UBERON:0002,,,sub struct 5,as-5,UBERON:0005,,,cell1,c1,,,,gene1,,,,,,,,,,,,,,,protein1,,,,,protein2,,,,,,,,,,,,,,,lipid1,,,,,metabolite1,,,,,ref1,,,,,,, +organ,,UBERON:1234,,,sub struct 2,,UBERON:0002,,,sub struct 5,as-5,UBERON:0005,,,cell2,c2,,,,gene1,,,,,gene2,,,,,gene3,,,,,,,,,,,,,,,proteo1,,,,,proteo2,,,,,lipid2,,,,,,,,,,ref2,,,,,,, +organ,,UBERON:1234,,,sub struct 2,,UBERON:0002,,,sub struct 5,as-5,UBERON:0005,,,cell3,c3,,,,gene1,,,,,gene3,,,,,,,,,,protein2,,,,,,,,,,proteo2,,,,,,,,,,,,,,,metabolite1,,,,,ref1,,,ref2,, +organ,,UBERON:1234,,,sub struct 2,,UBERON:0002,,,sub struct 6,as-6,UBERON:0006,,,cell3,c3,,,,gene1,,,,,gene3,,,,,,,,,,protein2,,,,,,,,,,proteo2,,,,,,,,,,,,,,,metabolite1,,,,,ref1,,,ref2,, diff --git a/demo-output.tree.txt b/sampledata/demo-output.tree.txt similarity index 100% rename from demo-output.tree.txt rename to sampledata/demo-output.tree.txt diff --git a/demo-output.xls b/sampledata/demo-output.xls similarity index 100% rename from demo-output.xls rename to sampledata/demo-output.xls diff --git a/demo-output.xls.dot b/sampledata/demo-output.xls.dot similarity index 100% rename from demo-output.xls.dot rename to sampledata/demo-output.xls.dot diff --git a/sampledata/placenta-input.tsv b/sampledata/placenta-input.tsv new file mode 100644 index 0000000..bc2af48 --- /dev/null +++ b/sampledata/placenta-input.tsv @@ -0,0 +1,153 @@ +Anatomical Structures, Cell Types and Biomarkers Table for Placenta v1.0 + +Author Name(s): Louise Laurent, Mana Parast, Kathleen Fisch +Author ORCID(s): 0000-0002-2095-7534; 000-0001-5963-2246; 0000-0002-0117-7444 +Reviewer(s): Drucilla Roberts +Reviewer ORCID(s): 0000-0002-9104-6674 +General Publication(s): +Data DOI: https://doi.org/10.48539/HBM446.WGLG.755 +Date: 5-6-2022 +Version Number: V1.0 +NAME (REF DOI) LABEL (REF DETAILS) ID (REF NOTES) NOTE ABBR TYPE CHILDREN CELLS GENES PROTEINS PROTEOFORMS LIPIDS METABOLITES FTU REFERENCES (NAME/DOI) +Placenta placenta UBERON:0001987 AS umbilical cord, fetal membranes, placental disc +umbilical cord umbilical cord UBERON:0002331 AS amnion, umbilical vein, umbilical arteries, mesenchyme of umbilical cord (Wharton's jelly) +fetal membranes AS amnion, chorion membrane, decidua +placental disc AS chorionic plate, basal plate, chorionic villous +umbilical vein umbilical vein UBERON:0002066 AS vascular endothelial cells, pericytes, vascular smooth muscle cells +umbilical arteries umbilical artery UBERON:0001310 AS vascular endothelial cells, pericytes, vascular smooth muscle cells +mesenchyme of umbilical cord (Wharton's jelly) mesenchyme of umbilical cord UBERON:0003422 Wharton's jelly AS mesenchymal stromal cell of Wharton's jelly +amnion amnion UBERON:0000305 AS amniotic ectoderm, amniotic mesoderm +chorion membrane chorion membrane UBERON:0003124 AS chorionic mesoderm, chorionic ectoderm (from chorion membrane) +chorionic plate chorionic plate UBERON:0004027 AS amniotic ectoderm, amniotic mesoderm, chorionic ectoderm (from chorionic plate), chorionic plate vessel +basal plate AS decidua extravillous trophoblast (interstitial) +chorionic villous chorionic villus UBERON:0007106 AS chorionic ectoderm (from chorionic plate), villous mesenchyme, stem villous vessel, villous capillary +amniotic ectoderm amnion epithelium UBERON:0003254 AS amnion epithelial cell (AEC) +amniotic mesoderm amniotic mesoderm UBERON:0003262 AS amnion mesenchymal stromal cell (AMSC) +chorionic ectoderm (from chorion membrane) trophoblast UBERON:0000088 from chorion membrane AS cytotrophoblast (CTB), extravillous trophoblast (EVT) +chorionic ectoderm (from chorionic plate) trophoblast UBERON:0000088 from chorionic plate AS cytotrophoblast (CTB), syncytiotrophoblast (STB), extravillous trophoblast (EVT) +chorionic mesoderm chorionic mesenchyme UBERON:0003265 AS chorionic mesenchymal stromal cell (CMSC) +chorionic plate vessel AS vascular endothelial cells, pericytes, vascular smooth muscle cells +villous mesenchyme AS Hofbauer cell (HC), placental stromal cell (PSC) +stem villous vessel AS vascular endothelial cells, pericytes, vascular smooth muscle cells +villous capillary AS placental microvascular endothelial cells, pericytes +decidua decidua UBERON:0002450 AS endometrial gland, endometrial stroma, decidual blood vessel, decidual lymphatic vessel +endometrial gland endometrial gland UBERON:0002451 AS endometrial epithelial cell +endometrial stroma endometrial stroma UBERON:0002337 AS endometrial stromal cell, uterine NK cell, uterine macrophage, regulatory T cell, cytotoxic T cell, B cell +decidual lymphatic vessel AS lymphatic endothelial cell +decidual blood vessel endometrial blood vessel UBERON:0015172 AS endometrial microvascular endothelial cell (EMEC), extravillous trophoblast (endovascular) +amnion epithelial cell (AEC) epithelial cell of amnion UBERON:0002536 CT KRT7, POU5F1, SOX2 SSEA3 DOI: 10.1016/j.jim.2003.03.001, DOI: 10.1053/plac.2000.0559, doi.org/10.1095/biolreprod.106.055244, doi: 10.1016/j.jri.2009.02.007, doi:10.1371/journal.pone.0146082, doi: 10.1016/j.jri.2009.02.007, doi:10.1371/journal.pone.0146082, doi: 10.1016/j.jri.2009.02.007, doi:10.17772/gp/1673, doi:10.1371/journal.pone.0146082 +amnion mesenchymal stromal cell (AMSC) CT CD44, THY1, ENG, NT5E doi: 10.3390/cells1041061, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod51.4.739, DOI: 10.1095/biolreprod.108.075226, doi.org/10.1182/blood.V74.2.751.751, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1093/humrep/den051, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1 +chorionic mesenchymal stromal cell (CMSC) CT CD44, THY1, ENG, NT5E, NCAM1 doi: 10.3390/cells1041061, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod51.4.739, DOI: 10.1095/biolreprod.108.075226, doi.org/10.1182/blood.V74.2.751.751, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1093/humrep/den051, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, doi: 10.5966/sctm.2015-0022, doi: 10.1016/j.jcyt.2017.03.001, PMID: 1697563 +placental stromal cell (PSC) CT CD44, THY1, ENG, NT5E doi: 10.3390/cells1041061, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod51.4.739, DOI: 10.1095/biolreprod.108.075226, doi.org/10.1182/blood.V74.2.751.751, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1093/humrep/den051, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1 +extravillous trophoblast (EVT) extravillous trophoblast CL:0008036 CT HLAG, KRT7, MCAM, PLAC8 doi.org/10.1016/0198-8859(93)90138-Q, DOI: 10.1016/j.jim.2003.03.001, DOI: 10.1053/plac.2000.0559, doi.org/10.1095/biolreprod.106.055244, PMID: 8804361, doi: 10.1155/2021/6662201, doi: 10.1093/humrep/dem265, DOI: 10.1242/dev.148932 +extravillous trophoblast (interstitial) extravillous trophoblast CL:0008036 CT HLAG, KRT7, MCAM, PLAC8 doi.org/10.1016/0198-8859(93)90138-Q, DOI: 10.1016/j.jim.2003.03.001, DOI: 10.1053/plac.2000.0559, doi.org/10.1095/biolreprod.106.055244, PMID: 8804361, doi: 10.1155/2021/6662201, doi: 10.1093/humrep/dem265, DOI: 10.1242/dev.148932 +extravillous trophoblast (endovascular) extravillous trophoblast CL:0008036 CT HLAG, KRT7, MCAM, CDH5 doi.org/10.1016/0198-8859(93)90138-Q, DOI: 10.1016/j.jim.2003.03.001, DOI: 10.1053/plac.2000.0559, doi.org/10.1095/biolreprod.106.055244, PMID: 8804361, doi: 10.1155/2021/6662201, doi: 10.1093/humrep/dem265, doi: 10.1172/JCI119387 +syncytiotrophoblast (STB) syncytiotrophoblast CL:0000525 CT CGB3, CSH1, PSG4, KRT7, EGFR DOI: 10.1146/annurev.bi.50.070181.002341, doi: 10.1056/NEJM197007232830408, doi: 10.1007/BF01628222, DOI: 10.1016/j.jim.2003.03.001, DOI: 10.1053/plac.2000.0559, doi.org/10.1095/biolreprod.106.055244, doi.org/10.1016/S0143-4004(05)80438-2, doi.org/10.1016/S0143-4004(05)80438-2 +cytotrophoblast (CTB) cytotrophoblast CL:0000523 CT EGFR, TP63, KRT7 doi.org/10.1016/S0143-4004(05)80438-2, doi.org/10.1016/S0143-4004(05)80438-2, doi: 10.1016/j.ajpath.2014.08.006, DOI: 10.1016/j.jim.2003.03.001, DOI: 10.1053/plac.2000.0559, doi.org/10.1095/biolreprod.106.055244 +placental microvascular endothelial cells placental villous capillary endothelial cell CL:2000062 CT MCAM, VWF, ESR2, RARA, RXRA PMID: 8804361, doi: 10.1155/2021/6662201, doi: 10.1093/humrep/dem265, doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2, DOI: 10.1093/oxfordjournals.humrep.a136040, doi.org/10.1016/j.ajog.2009.01.025 +Hofbauer cell (HC) Hofbauer cell CL:3000001 CT CD163, FCGR1A, CD68 doi: 10.1016/j.placenta.2007.11.003, DOI: 10.1053/plac.2000.0559, PMID: 8014121 +endometrial epithelial cell CT KRT18, KRT19, EPCAM, FUT4 DOI: 10.1177/1933719118756745, DOI: 10.1177/1933719118756745, doi: 10.1186/s13287-018-0962-6, DOI: 10.1093/humrep/det285 +endometrial stromal cell stromal cell of endometrium CL:0002255 CT CD44, THY1, ENG, MME doi: 10.3390/cells1041061, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod51.4.739, DOI: 10.1095/biolreprod.108.075226, doi.org/10.1182/blood.V74.2.751.751, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1093/humrep/den051, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod.108.075226, doi: 10.1016/s1472-6483(10)61745-2 +uterine NK cell CT NCAM1 doi: 10.5966/sctm.2015-0022, doi: 10.1016/j.jcyt.2017.03.001 +uterine macrophage CT CD68, ITGAX, CD209, MRC1 DOI: 10.1053/plac.2000.0559, doi: 10.1038/s41423-018-0008-0, doi: 10.1371/journal.pone.0002078, doi: 10.1371/journal.pone.0002078 +regulatory T cell regulatory T cell CL:0000815 CT FOXP3 DOI: 10.1038/ni904 +cytotoxic T cell cytotoxic T cell CL:0000910 CT CD8A, CD28 PMID: 1672332, PMID: 7579453 +B cell B cell CL:0000236 CT CD44, SDC1, HLA-DRA doi: 10.3390/cells1041061, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod51.4.739, DOI: 10.1095/biolreprod.108.075226, doi.org/10.1182/blood.V74.2.751.751, doi: 10.1091/mbc.1.1.27, doi:10.1093/intimm/7.7.1087 +endometrial microvascular endothelial cell (EMEC) endometrial microvascular endothelial cells CL:2000091 CT MCAM, VWF PMID: 8804361, doi: 10.1155/2021/6662201, doi: 10.1093/humrep/dem265, doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2, DOI: 10.1093/oxfordjournals.humrep.a136040 +mesenchymal stromal cell of Wharton's jelly mesenchymal stem cell of Wharton's jelly CL:0002568 CT CD44, THY1, ENG, NT5E doi: 10.3390/cells1041061, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod51.4.739, DOI: 10.1095/biolreprod.108.075226, doi.org/10.1182/blood.V74.2.751.751, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1093/humrep/den051, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1, DOI: 10.1095/biolreprod.108.075226, doi: 10.3390/cells1041061, doi: 10.5966/sctm.2015-0022, doi: 10.3346/jkms.2012.27.8.857, doi: 10.1016/j.jcyt.2017.03.001, doi: 10.1186/s13287-017-0757-1 +vascular endothelial cells blood vessel endothelial cell CL:0000071 CT MCAM, VWF, PECAM1 PMID: 8804361, doi: 10.1155/2021/6662201, doi: 10.1093/humrep/dem265, doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2, DOI: 10.1093/oxfordjournals.humrep.a136040, doi.org/10.1371/journal.pone.0169849, doi.org/10.1371/journal.pone.0169849 +pericytes pericyte cell CL:0000669 CT DES, ACTA2, PDGFRB, CSPG4 DOI: 10.1016/0014-4800(90)90037-e, DOI: 10.1007/s00441-003-0745-x, doi: 10.1038/ng.2007.6., DOI: 10.1007/s00441-003-0745-x, DOI: 10.1007/s00441-003-0745-x, DOI: 10.1007/s00441-003-0745-x +vascular smooth muscle cells vascular associated smooth muscle cell CL:0000359 CT DES, ACTA2 DOI: 10.1016/0014-4800(90)90037-e, DOI: 10.1007/s00441-003-0745-x, doi: 10.1038/ng.2007.6., DOI: 10.1007/s00441-003-0745-x +lymphatic endothelial cell endothelial cell of lymphatic vessel CL:0002138 CT PECAM1, PDPN doi.org/10.1371/journal.pone.0169849, doi.org/10.1371/journal.pone.0169849, doi.org/10.1371/journal.pone.0169849 +POU5F1 POU class 5 homeobox 1 HGNC:9221 Gene +SOX2 SRY-box transcription factor 2 HGNC:11195 Gene +CD44 CD44 molecule (Indian blood group) HGNC:1681 Gene +THY1 Thy-1 cell surface antigen HGNC:11801 Gene +ENG endoglin HGNC:3349 Gene +NT5E 5'-nucleotidase ecto HGNC:8021 Gene +NCAM1 neural cell adhesion molecule 1 HGNC: 7656 Gene +CGB3 chorionic gonadotropin subunit beta 3 HGNC:1886 Gene +CSH1 chorionic somatomammotropin hormone 1 HGNC:2440 Gene +PSG4 pregnancy specific beta-1-glycoprotein 4 HGNC:9521 Gene +KRT7 keratin 7 HGNC:6445 Gene +HLAG major histocompatibility complex, class I, G HGNC:4964 Gene +MCAM melanoma cell adhesion molecule HGNC:6934 Gene +EGFR epidermal growth factor receptor HGNC:3236 Gene +TP63 tumor protein p63 HGNC:15979 Gene +VWF von Willebrand factor HGNC:12726 Gene +ESR2 estrogen receptor 2 HGNC:3468 Gene +RARA retinoic acid receptor alpha HGNC:9864 Gene +RXRA retinoid X receptor alpha HGNC:10477 Gene +CD163 CD163 molecule HGNC:1631 Gene +FCGR1A Fc gamma receptor Ia HGNC:3613 Gene +CD68 CD68 molecule HGNC:1693 Gene +KRT18 keratin 18 HGNC:6427 Gene +KRT19 keratin 19 HGNC:6436 Gene +EPCAM epithelial cell adhesion molecule HGNC:11529 Gene +MME membrane metalloendopeptidase HGNC: 7154 Gene +CD13 alanyl aminopeptidase, membrane HGNC: 500 Gene +ITGAX integrin subunit alpha X HGNC:6152 Gene +CD209 CD209 molecule HGNC:1641 Gene +MRC1 mannose receptor C-type 1 HGNC:7228 Gene +FOXP3 forkhead box P3 HGNC:6106 Gene +CD8A CD8a molecule HGNC:1706 Gene +CD28 CD28 molecule HGNC:1653 Gene +SDC1 syndecan 1 HGNC:10658 Gene +HLA-DRA Major Histocompatibility Complex, Class II, DR Alpha HGNC: 4947 It appears that the well-recognized B-cell marker CD78/CDw78 is an antigen that is expressed as part of the MHC class II molecule Gene +PECAM1 platelet and endothelial cell adhesion molecule 1 HGNC: 8823 Gene +PDPN podoplanin HGNC: 29602 Gene +CDH5 cadherin 5 HGNC: 1764 Gene +PLAC8 placenta associated 8 HGNC: 19254 Gene +DES desmin HGNC: 2770 Gene +ACTA2 actin alpha 2, smooth muscle HGNC: 130 Gene +PDGFRB platelet derived growth factor receptor beta HGNC: 8804 Gene +CSPG4 chondroitin sulfate proteoglycan 4 HGNC: 2466 Gene +FUT4 Fucosyltransferase 4 HGNC: 4015 Gene +SSEA3 Stage-specific embryonic antigen-3 LM:LMSP0502AE00 Lipid +doi: 10.1016/j.jri.2009.02.007 doi: 10.1016/j.jri.2009.02.007 Reference +doi: 10.3390/cells1041061 doi: 10.3390/cells1041061 Reference +doi: 10.5966/sctm.2015-0022 doi: 10.5966/sctm.2015-0022 Reference +DOI: 10.1146/annurev.bi.50.070181.002341 DOI: 10.1146/annurev.bi.50.070181.002341 Reference +doi: 10.1056/NEJM197007232830408 doi: 10.1056/NEJM197007232830408 Reference +doi: 10.1007/BF01628222 doi: 10.1007/BF01628222 Reference +DOI: 10.1016/j.jim.2003.03.001 DOI: 10.1016/j.jim.2003.03.001 Reference +doi.org/10.1016/0198-8859(93)90138-Q doi.org/10.1016/0198-8859(93)90138-Q Reference +PMID: 8804361 PMID: 8804361 Reference +doi.org/10.1016/S0143-4004(05)80438-2 doi.org/10.1016/S0143-4004(05)80438-2 Reference +doi: 10.1016/j.ajpath.2014.08.006 doi: 10.1016/j.ajpath.2014.08.006 Reference +doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2 doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2 Reference +doi.org/10.1016/j.ajog.2009.01.025 doi.org/10.1016/j.ajog.2009.01.025 Reference +doi: 10.1016/j.placenta.2007.11.003 doi: 10.1016/j.placenta.2007.11.003 Reference +PMID: 8014121 PMID: 8014121 Reference +DOI: 10.1053/plac.2000.0559 DOI: 10.1053/plac.2000.0559 Reference +DOI: 10.1177/1933719118756745 DOI: 10.1177/1933719118756745 Reference +doi: 10.1186/s13287-018-0962-6 doi: 10.1186/s13287-018-0962-6 Reference +doi: 10.1016/s1472-6483(10)61745-2 doi: 10.1016/s1472-6483(10)61745-2 Reference +PMID: 1697563 PMID: 1697563 Reference +doi: 10.1038/s41423-018-0008-0 doi: 10.1038/s41423-018-0008-0 Reference +doi: 10.1371/journal.pone.0002078 doi: 10.1371/journal.pone.0002078 Reference +DOI: 10.1038/ni904 DOI: 10.1038/ni904 Reference +PMID: 1672332 PMID: 1672332 Reference +PMID: 7579453 PMID: 7579453 Reference +doi: 10.1091/mbc.1.1.27 doi: 10.1091/mbc.1.1.27 Reference +doi:10.1093/intimm/7.7.1087 doi:10.1093/intimm/7.7.1087 Reference +doi.org/10.1371/journal.pone.0169849 doi.org/10.1371/journal.pone.0169849 Reference +doi: 10.1172/JCI119387 doi: 10.1172/JCI119387 Reference +DOI: 10.1242/dev.148932 DOI: 10.1242/dev.148932 Reference +DOI: 10.1016/0014-4800(90)90037-e DOI: 10.1016/0014-4800(90)90037-e Reference +doi: 10.1038/ng.2007.6. doi: 10.1038/ng.2007.6. Reference +DOI: 10.1007/s00441-003-0745-x DOI: 10.1007/s00441-003-0745-x Reference +DOI: 10.1093/humrep/det285 DOI: 10.1093/humrep/det285 Reference +DOI: 10.1093/oxfordjournals.humrep.a136040 DOI: 10.1093/oxfordjournals.humrep.a136040 Reference +doi: 10.1155/2021/6662201 doi: 10.1155/2021/6662201 Reference +DOI: 10.1095/biolreprod.108.075226 DOI: 10.1095/biolreprod.108.075226 Reference +doi: 10.1186/s13287-017-0757-1 doi: 10.1186/s13287-017-0757-1 Reference +doi.org/10.1095/biolreprod.106.055244 doi.org/10.1095/biolreprod.106.055244 Reference +doi.org/10.1182/blood.V74.2.751.751 doi.org/10.1182/blood.V74.2.751.751 Reference +DOI: 10.1093/humrep/den051 DOI: 10.1093/humrep/den051 Reference +DOI: 10.1095/biolreprod51.4.739 DOI: 10.1095/biolreprod51.4.739 Reference +doi: 10.1016/j.jcyt.2017.03.001 doi: 10.1016/j.jcyt.2017.03.001 Reference +doi: 10.3346/jkms.2012.27.8.857 doi: 10.3346/jkms.2012.27.8.857 Reference +doi: 10.1093/humrep/dem265 doi: 10.1093/humrep/dem265 Reference +doi:10.1371/journal.pone.0146082 doi:10.1371/journal.pone.0146082 Reference +doi:10.17772/gp/1673 doi:10.17772/gp/1673 Reference diff --git a/sampledata/placenta-output.csv b/sampledata/placenta-output.csv new file mode 100644 index 0000000..44c67b2 --- /dev/null +++ b/sampledata/placenta-output.csv @@ -0,0 +1,64 @@ +"Anatomical Structures, Cell Types and Biomarkers Table for Placenta v1.0",,,,,,,,,,,,,, +,,,,,,,,,,,,,, +Author Name(s):,"Louise Laurent, Mana Parast, Kathleen Fisch",,,,,,,,,,,,, +Author ORCID(s):,0000-0002-2095-7534; 000-0001-5963-2246; 0000-0002-0117-7444,,,,,,,,,,,,, +Reviewer(s):,Drucilla Roberts,,,,,,,,,,,,, +Reviewer ORCID(s):,0000-0002-9104-6674 ,,,,,,,,,,,,, +General Publication(s):,,,,,,,,,,,,,, +Data DOI:,https://doi.org/10.48539/HBM446.WGLG.755,,,,,,,,,,,,, +Date:,5-6-2022,,,,,,,,,,,,, +Version Number:,V1.0,,,,,,,,,,,,, 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10.1038/s41423-018-0008-0,,doi: 10.1371/journal.pone.0002078,doi: 10.1371/journal.pone.0002078,,doi: 10.1371/journal.pone.0002078,doi: 10.1371/journal.pone.0002078,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,fetal membranes,,,,,decidua,decidua,UBERON:0002450,,,endometrial stroma,endometrial stroma,UBERON:0002337,,,,,,,,regulatory T cell,regulatory T cell ,CL:0000815,,,FOXP3,forkhead box P3,HGNC:6106,,,,,,,,,,,,,,,,,,,,,,,,,,,,DOI: 10.1038/ni904,DOI: 10.1038/ni904,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,fetal membranes,,,,,decidua,decidua,UBERON:0002450,,,endometrial stroma,endometrial stroma,UBERON:0002337,,,,,,,,cytotoxic T cell,cytotoxic T cell,CL:0000910,,,CD8A,CD8a molecule,HGNC:1706,,,CD28,CD28 molecule,HGNC:1653,,,,,,,,,,,,,,,,,,,,,,,PMID: 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10.1093/oxfordjournals.humrep.a136040,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,fetal membranes,,,,,decidua,decidua,UBERON:0002450,,,decidual blood vessel,endometrial blood vessel,UBERON:0015172,,,,,,,,extravillous trophoblast (endovascular),extravillous trophoblast,CL:0008036,,,HLAG,"major histocompatibility complex, class I, G",HGNC:4964,,,KRT7,keratin 7,HGNC:6445,,,MCAM,melanoma cell adhesion molecule,HGNC:6934,,,CDH5,cadherin 5,HGNC: 1764,,,,,,,,,,,,,doi.org/10.1016/0198-8859(93)90138-Q,doi.org/10.1016/0198-8859(93)90138-Q,,DOI: 10.1016/j.jim.2003.03.001,DOI: 10.1016/j.jim.2003.03.001,,DOI: 10.1053/plac.2000.0559,DOI: 10.1053/plac.2000.0559,,doi.org/10.1095/biolreprod.106.055244,doi.org/10.1095/biolreprod.106.055244,,PMID: 8804361,PMID: 8804361,,doi: 10.1155/2021/6662201,doi: 10.1155/2021/6662201,,doi: 10.1093/humrep/dem265,doi: 10.1093/humrep/dem265,,doi: 10.1172/JCI119387,doi: 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amnion,UBERON:0002536,,,KRT7,keratin 7,HGNC:6445,,,POU5F1,POU class 5 homeobox 1,HGNC:9221,,,SOX2,SRY-box transcription factor 2,HGNC:11195,,,,,,,,,,,,,SSEA3,Stage-specific embryonic antigen-3,LM:LMSP0502AE00,,,DOI: 10.1016/j.jim.2003.03.001,DOI: 10.1016/j.jim.2003.03.001,,DOI: 10.1053/plac.2000.0559,DOI: 10.1053/plac.2000.0559,,doi.org/10.1095/biolreprod.106.055244,doi.org/10.1095/biolreprod.106.055244,,doi: 10.1016/j.jri.2009.02.007,doi: 10.1016/j.jri.2009.02.007,,doi:10.1371/journal.pone.0146082,doi:10.1371/journal.pone.0146082,,doi: 10.1016/j.jri.2009.02.007,doi: 10.1016/j.jri.2009.02.007,,doi:10.1371/journal.pone.0146082,doi:10.1371/journal.pone.0146082,,doi: 10.1016/j.jri.2009.02.007,doi: 10.1016/j.jri.2009.02.007,,doi:10.17772/gp/1673,doi:10.17772/gp/1673,,doi:10.1371/journal.pone.0146082,doi:10.1371/journal.pone.0146082,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,fetal 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endothelial cells,placental villous capillary endothelial cell,CL:2000062,,,MCAM,melanoma cell adhesion molecule,HGNC:6934,,,VWF,von Willebrand factor,HGNC:12726,,,ESR2,estrogen receptor 2,HGNC:3468,,,RARA,retinoic acid receptor alpha,HGNC:9864,,,RXRA,retinoid X receptor alpha,HGNC:10477,,,,,,,,PMID: 8804361,PMID: 8804361,,doi: 10.1155/2021/6662201,doi: 10.1155/2021/6662201,,doi: 10.1093/humrep/dem265,doi: 10.1093/humrep/dem265,,doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2,doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2,,DOI: 10.1093/oxfordjournals.humrep.a136040,DOI: 10.1093/oxfordjournals.humrep.a136040,,doi.org/10.1016/j.ajog.2009.01.025,doi.org/10.1016/j.ajog.2009.01.025,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,chorionic villous,chorionic villus,UBERON:0007106,,,villous capillary,,,,,,,,,,pericytes,pericyte cell,CL:0000669,,,DES,desmin,HGNC: 2770,,,ACTA2,"actin alpha 2, smooth muscle",HGNC: 130,,,PDGFRB,platelet derived growth factor receptor beta,HGNC: 8804,,,CSPG4,chondroitin sulfate proteoglycan 4,HGNC: 2466 ,,,,,,,,,,,,,DOI: 10.1016/0014-4800(90)90037-e,DOI: 10.1016/0014-4800(90)90037-e,,DOI: 10.1007/s00441-003-0745-x,DOI: 10.1007/s00441-003-0745-x,,doi: 10.1038/ng.2007.6.,doi: 10.1038/ng.2007.6.,,DOI: 10.1007/s00441-003-0745-x,DOI: 10.1007/s00441-003-0745-x,,DOI: 10.1007/s00441-003-0745-x,DOI: 10.1007/s00441-003-0745-x,,DOI: 10.1007/s00441-003-0745-x,DOI: 10.1007/s00441-003-0745-x,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,endometrial gland,endometrial gland,UBERON:0002451,,,endometrial epithelial cell,,,,,KRT18,keratin 18,HGNC:6427,,,KRT19,keratin 19,HGNC:6436,,,EPCAM,epithelial cell adhesion molecule,HGNC:11529,,,FUT4,Fucosyltransferase 4,HGNC: 4015,,,,,,,,,,,,,DOI: 10.1177/1933719118756745,DOI: 10.1177/1933719118756745,,DOI: 10.1177/1933719118756745,DOI: 10.1177/1933719118756745,,doi: 10.1186/s13287-018-0962-6,doi: 10.1186/s13287-018-0962-6,,DOI: 10.1093/humrep/det285,DOI: 10.1093/humrep/det285,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,endometrial stroma,endometrial stroma,UBERON:0002337,,,endometrial stromal cell,stromal cell of endometrium,CL:0002255,,,CD44,CD44 molecule (Indian blood group),HGNC:1681,,,THY1,Thy-1 cell surface antigen,HGNC:11801,,,ENG,endoglin,HGNC:3349,,,MME,membrane metalloendopeptidase,HGNC: 7154,,,,,,,,,,,,,doi: 10.3390/cells1041061,doi: 10.3390/cells1041061,,doi: 10.1016/j.jcyt.2017.03.001,doi: 10.1016/j.jcyt.2017.03.001,,doi: 10.1186/s13287-017-0757-1,doi: 10.1186/s13287-017-0757-1,,DOI: 10.1095/biolreprod51.4.739,DOI: 10.1095/biolreprod51.4.739,,DOI: 10.1095/biolreprod.108.075226,DOI: 10.1095/biolreprod.108.075226,,doi.org/10.1182/blood.V74.2.751.751,doi.org/10.1182/blood.V74.2.751.751,,doi: 10.3390/cells1041061,doi: 10.3390/cells1041061,,doi: 10.5966/sctm.2015-0022,doi: 10.5966/sctm.2015-0022,,doi: 10.3346/jkms.2012.27.8.857,doi: 10.3346/jkms.2012.27.8.857,,doi: 10.1016/j.jcyt.2017.03.001,doi: 10.1016/j.jcyt.2017.03.001,,doi: 10.1186/s13287-017-0757-1,doi: 10.1186/s13287-017-0757-1,,DOI: 10.1093/humrep/den051,DOI: 10.1093/humrep/den051,,DOI: 10.1095/biolreprod.108.075226,DOI: 10.1095/biolreprod.108.075226,,doi: 10.3390/cells1041061,doi: 10.3390/cells1041061,,doi: 10.5966/sctm.2015-0022,doi: 10.5966/sctm.2015-0022,,doi: 10.3346/jkms.2012.27.8.857,doi: 10.3346/jkms.2012.27.8.857,,doi: 10.1016/j.jcyt.2017.03.001,doi: 10.1016/j.jcyt.2017.03.001,,doi: 10.1186/s13287-017-0757-1,doi: 10.1186/s13287-017-0757-1,,DOI: 10.1095/biolreprod.108.075226,DOI: 10.1095/biolreprod.108.075226,,doi: 10.1016/s1472-6483(10)61745-2,doi: 10.1016/s1472-6483(10)61745-2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,endometrial stroma,endometrial stroma,UBERON:0002337,,,uterine NK cell,,,,,NCAM1,neural cell adhesion molecule 1,HGNC: 7656,,,,,,,,,,,,,,,,,,,,,,,,,,,,doi: 10.5966/sctm.2015-0022,doi: 10.5966/sctm.2015-0022,,doi: 10.1016/j.jcyt.2017.03.001,doi: 10.1016/j.jcyt.2017.03.001,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,endometrial stroma,endometrial stroma,UBERON:0002337,,,uterine macrophage,,,,,CD68,CD68 molecule,HGNC:1693,,,ITGAX,integrin subunit alpha X,HGNC:6152,,,CD209,CD209 molecule,HGNC:1641,,,MRC1,mannose receptor C-type 1,HGNC:7228,,,,,,,,,,,,,DOI: 10.1053/plac.2000.0559,DOI: 10.1053/plac.2000.0559,,doi: 10.1038/s41423-018-0008-0,doi: 10.1038/s41423-018-0008-0,,doi: 10.1371/journal.pone.0002078,doi: 10.1371/journal.pone.0002078,,doi: 10.1371/journal.pone.0002078,doi: 10.1371/journal.pone.0002078,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,endometrial stroma,endometrial stroma,UBERON:0002337,,,regulatory T cell,regulatory T cell ,CL:0000815,,,FOXP3,forkhead box P3,HGNC:6106,,,,,,,,,,,,,,,,,,,,,,,,,,,,DOI: 10.1038/ni904,DOI: 10.1038/ni904,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,endometrial stroma,endometrial stroma,UBERON:0002337,,,cytotoxic T cell,cytotoxic T cell,CL:0000910,,,CD8A,CD8a molecule,HGNC:1706,,,CD28,CD28 molecule,HGNC:1653,,,,,,,,,,,,,,,,,,,,,,,PMID: 1672332,PMID: 1672332,,PMID: 7579453,PMID: 7579453,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,endometrial stroma,endometrial stroma,UBERON:0002337,,,B cell,B cell,CL:0000236,,,CD44,CD44 molecule (Indian blood group),HGNC:1681,,,SDC1,syndecan 1,HGNC:10658,,,HLA-DRA,"Major Histocompatibility Complex, Class II, DR Alpha",HGNC: 4947,It appears that the well-recognized B-cell marker CD78/CDw78 is an antigen that is expressed as part of the MHC class II molecule,,,,,,,,,,,,,,,,,doi: 10.3390/cells1041061,doi: 10.3390/cells1041061,,doi: 10.1016/j.jcyt.2017.03.001,doi: 10.1016/j.jcyt.2017.03.001,,doi: 10.1186/s13287-017-0757-1,doi: 10.1186/s13287-017-0757-1,,DOI: 10.1095/biolreprod51.4.739,DOI: 10.1095/biolreprod51.4.739,,DOI: 10.1095/biolreprod.108.075226,DOI: 10.1095/biolreprod.108.075226,,doi.org/10.1182/blood.V74.2.751.751,doi.org/10.1182/blood.V74.2.751.751,,doi: 10.1091/mbc.1.1.27,doi: 10.1091/mbc.1.1.27,,doi:10.1093/intimm/7.7.1087,doi:10.1093/intimm/7.7.1087,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,decidual blood vessel,endometrial blood vessel,UBERON:0015172,,,endometrial microvascular endothelial cell (EMEC),endometrial microvascular endothelial cells,CL:2000091,,,MCAM,melanoma cell adhesion molecule,HGNC:6934,,,VWF,von Willebrand factor,HGNC:12726,,,,,,,,,,,,,,,,,,,,,,,PMID: 8804361,PMID: 8804361,,doi: 10.1155/2021/6662201,doi: 10.1155/2021/6662201,,doi: 10.1093/humrep/dem265,doi: 10.1093/humrep/dem265,,doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2,doi: 10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2,,DOI: 10.1093/oxfordjournals.humrep.a136040,DOI: 10.1093/oxfordjournals.humrep.a136040,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,decidual blood vessel,endometrial blood vessel,UBERON:0015172,,,extravillous trophoblast (endovascular),extravillous trophoblast,CL:0008036,,,HLAG,"major histocompatibility complex, class I, G",HGNC:4964,,,KRT7,keratin 7,HGNC:6445,,,MCAM,melanoma cell adhesion molecule,HGNC:6934,,,CDH5,cadherin 5,HGNC: 1764,,,,,,,,,,,,,doi.org/10.1016/0198-8859(93)90138-Q,doi.org/10.1016/0198-8859(93)90138-Q,,DOI: 10.1016/j.jim.2003.03.001,DOI: 10.1016/j.jim.2003.03.001,,DOI: 10.1053/plac.2000.0559,DOI: 10.1053/plac.2000.0559,,doi.org/10.1095/biolreprod.106.055244,doi.org/10.1095/biolreprod.106.055244,,PMID: 8804361,PMID: 8804361,,doi: 10.1155/2021/6662201,doi: 10.1155/2021/6662201,,doi: 10.1093/humrep/dem265,doi: 10.1093/humrep/dem265,,doi: 10.1172/JCI119387,doi: 10.1172/JCI119387,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Placenta,placenta,UBERON:0001987,,,placental disc,,,,,basal plate,,,,,decidua,decidua,UBERON:0002450,,,decidual lymphatic vessel,,,,,lymphatic endothelial cell,endothelial cell of lymphatic vessel,CL:0002138,,,PECAM1,platelet and endothelial cell adhesion molecule 1,HGNC: 8823 ,,,PDPN,podoplanin,HGNC: 29602,,,,,,,,,,,,,,,,,,,,,,,doi.org/10.1371/journal.pone.0169849,doi.org/10.1371/journal.pone.0169849,,doi.org/10.1371/journal.pone.0169849,doi.org/10.1371/journal.pone.0169849,,doi.org/10.1371/journal.pone.0169849,doi.org/10.1371/journal.pone.0169849,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,