cellosaurus.readme

CELL
	pub
 	species
		disease
		sex
        age
		category/type
			anatomy
				marker/allele


xmlstarlet el -a cellosaurus.xml | sort -u > cellosaurus.xpath

xpath2dot.awk cellosaurus.xpath > cellosaurus.gv

dot-T png cellosaurus.gv > cellosaurus.png

wc -l < cellosaurus.xpath
119

###############################################################
# cell line identifier
Cellosaurus/cell-line-list/cell-line/accession-list
Cellosaurus/cell-line-list/cell-line/accession-list/accession
Cellosaurus/cell-line-list/cell-line/accession-list/accession/@type
	where @type=primary


xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/accession-list/accession[@type='primary']" \
	cellosaurus.xml | cut -f1 -d '_' | sort | uniq -c
 101,528 CVCL


# unique?
xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/accession-list/accession[@type='primary']" \
	cellosaurus.xml | sort -u| wc -l
101,528


-----------------------------------------------------
Cellosaurus/cell-line-list/cell-line/
	@category=
	@sex=
 	@age=

xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/@category"  \
	cellosaurus.xml | sort | uniq -c | sort -nr
  43853 Transformed cell line
  18284 Cancer cell line
  13479 Embryonic stem cell
   8553 Finite cell line
   7234 Induced pluripotent stem cell
   4264 Hybridoma
   4123 Spontaneously immortalized cell line
    596 Hybrid cell line
    307 Telomerase immortalized cell line
    286 Conditionally immortalized cell line
    187 Undefined cell line type
    170 Adult stem cell
    135 Factor-dependent cell line
     57 Stromal cell line


xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/@sex"  \
	cellosaurus.xml | sort | uniq -c | sort -nr
  46680 Male
  38148 Female
   4041 Sex unspecified
     87 Sex ambiguous
     37 Mixed sex


# yuck
# try with numerals and ranges removed
# Years, Months, Weeks, Days
xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/@age"  \
	cellosaurus.xml | tr -d "0123456789-" | sort | uniq -c | sort -nr
  39066 Y
  14163 Age unspecified
  13536 Blastocyst stage
   1964 Adult
   1041 YM
    655 M
    645 Fetus
    632 FW
    505 D
    299 Embryo
    166 &lt;M
    123 W
     91 Children
     89 Third instar larval stage
     82 Embryonic stage
     78 &lt;D
     57 FD
     39 Late embryonic stage
     28 Pupal stage
     28 MW
     26 Dorsal closure stage
     21 Larva
     15 FM
     14 Neonate larva
     13 First instar larval stage
     11 &lt;Y
      9 Yearling
      8 Juvenile
      8 &gt;Y
      7 &gt;FD
      7 Early tailbud stage
      6 Tadpole stage
      6 Extended germ band stage
      6 Embryo/neonate larva
      5 Prenatal stage
      5 Adult frog stage
      4 Moulting nymph
      4 Fawn
      3 Newborn
      3 Morula stage
      3 Fry
      3 Adult stage
      2 Somite stage
      2 Prepubertal
      2 Moulting larva
      2 MD
      2 Larval stage
      2 Fingerling
      2 Fifth instar larval stage
      2 Blastula stage
      1 Prim stage
      1 NF stage
      1 Late pupal stage
      1 Fourth instar larval stage
      1 Embryonic stage
      1 Early extended germ band stage
      1 Calf
      1 Blastula high stage

# would like a staging ontology,




# species
Cellosaurus/cell-line-list/cell-line/species-list/cv-term
Cellosaurus/cell-line-list/cell-line/species-list/cv-term/@accession
Cellosaurus/cell-line-list/cell-line/species-list/cv-term/@terminology

xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/species-list/cv-term"  \
	cellosaurus.xml | sort | uniq -c | sort -nr
  74534 Homo sapiens
  19137 Mus musculus
   1908 Rattus norvegicus
   1580 Cricetulus griseus
    571 Canis lupus familiaris
    357 Gallus gallus
    272 Bos taurus
    244 Drosophila melanogaster
    230 Pan troglodytes
    183 Sus scrofa
    178 Felis catus
    157 Mesocricetus auratus
    109 Oryctolagus cuniculus
     86 Macaca mulatta
     69 Chlorocebus aethiops
     62 Ovis aries
     56 Equus caballus
... and lots more

xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/species-list/cv-term"  \
	cellosaurus.xml | sort -u | wc -l
590

(check if we want all 590 species  ... most likely do)


# diseases
Cellosaurus/cell-line-list/cell-line/disease-list
Cellosaurus/cell-line-list/cell-line/disease-list/cv-term
Cellosaurus/cell-line-list/cell-line/disease-list/cv-term/@accession
Cellosaurus/cell-line-list/cell-line/disease-list/cv-term/@terminology

xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/disease-list/cv-term"  \
	cellosaurus.xml | sort | uniq -c | sort -nr
   4367 Type 2 diabetes mellitus
   2789 Parkinson's disease
   1889 Amyotrophic lateral sclerosis
   1848 Melanoma
   1497 Huntington's disease
   1021 Seizure disorder
   1018 Ischemic cerebrovascular accident
    535 Neuroblastoma
    496 Lung adenocarcinoma
    489 Small cell lung carcinoma
    474 Intracranial aneurysm
    431 Human papillomavirus-related endocervical adenocarcinoma
    424 Glioblastoma
    416 Osteosarcoma
    410 Subarachnoid hemorrhage
    410 Colon adenocarcinoma
    314 Dilated cardiomyopathy
    287 Alzheimer's disease

xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/disease-list/cv-term" \
	cellosaurus.xml | sort -u | wc -l
1617

xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/disease-list/cv-term/@accession"  \
	cellosaurus.xml | cut -f1 -d '_' | sort | uniq -c | sort -nr | head
   4367 C26747
   2789 C26845
   1889 C34373
   1848 C3224
   1497 C82342
   1021 C3020
   1018 C95802
    535 C3270
    496 C3512
    490 C4917

# seem to be NCIt terms (keep as is & let clique leader translate)


# anatomy?  from their faq.

```
-Tissue: Not yet possible.
We plan to add the tissue of origin using Uberon as the standardization resource,
but this will not take place until 2018.
```


# markers/alleles
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/@conflict
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/@id
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data/alleles


 xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/@id" \
	cellosaurus.xml | sort | uniq -c | sort -nr | head
   5393 vWA
   5387 Amelogenin
   5343 D7S820
   5332 D5S818
   5331 D13S317
   5298 TH01
   5264 CSF1PO
   5263 TPOX
   5068 D16S539
   2427 FGA
...

pretty short list, only 41 markers


xmlstarlet sel -t -v "//Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data/alleles"  \
	cellosaurus.xml | sort | uniq -c | sort -nr | head
   3814 11,12
   3699 11
   3344 X
   3323 12
   2117 8,11
   2103 8
   2095 X,Y
   2065 10,11
   1765 10,12
   1607 9
...

hmmm, looks more like chromosomes to me

prefers "alleles" were per chromosome

#############################################################
# pubs
Cellosaurus/publication-list/publication/xref-list/xref
Cellosaurus/publication-list/publication/xref-list/xref/@accession
Cellosaurus/publication-list/publication/xref-list/xref/@category
Cellosaurus/publication-list/publication/xref-list/xref/@database
Cellosaurus/publication-list/publication/xref-list/xref/url

# category
 26,054 Reference resources

# database
xmlstarlet sel -t -v "//Cellosaurus/publication-list/publication/xref-list/xref/@database"  \
	cellosaurus.xml | sort | uniq -c | sort -nr
  13584 PubMed
  11348 DOI
    736 Patent
    386 CelloPub


# accession

all but one (10.1007/BF01753729) is unique

xmlstarlet sel -t -v "//Cellosaurus/publication-list/publication/xref-list/xref/@accession"  \
	cellosaurus.xml | sort | uniq -c | wc -l
26,053

#############################################################

curl -s https://gist.githubusercontent.com/TomConlin/4392fc172dc2023bda7cf6f0f5d0f280/raw/b3dc6650bcc8092b3439f6754adcacf5f5237258/cellosaurus.xpath| xpath2dot.awk -v ORIENT="UD" | dot -T png > cellosaurus_xpath.png

cellosaurus.xpath

Cellosaurus
Cellosaurus/cell-line-list
Cellosaurus/cell-line-list/cell-line
Cellosaurus/cell-line-list/cell-line/accession-list
Cellosaurus/cell-line-list/cell-line/accession-list/accession
Cellosaurus/cell-line-list/cell-line/accession-list/accession/@type
Cellosaurus/cell-line-list/cell-line/@age
Cellosaurus/cell-line-list/cell-line/@category
Cellosaurus/cell-line-list/cell-line/comment-list
Cellosaurus/cell-line-list/cell-line/comment-list/comment
Cellosaurus/cell-line-list/cell-line/comment-list/comment/@category
Cellosaurus/cell-line-list/cell-line/comment-list/comment/cv-term
Cellosaurus/cell-line-list/cell-line/comment-list/comment/cv-term/@accession
Cellosaurus/cell-line-list/cell-line/comment-list/comment/cv-term/@terminology
Cellosaurus/cell-line-list/cell-line/comment-list/comment/method
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref/@accession
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref/@category
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref/@database
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref/property-list
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref/property-list/property
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref/property-list/property/@name
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref/property-list/property/@value
Cellosaurus/cell-line-list/cell-line/comment-list/comment/xref-list/xref/url
Cellosaurus/cell-line-list/cell-line/derived-from
Cellosaurus/cell-line-list/cell-line/derived-from/cv-term
Cellosaurus/cell-line-list/cell-line/derived-from/cv-term/@accession
Cellosaurus/cell-line-list/cell-line/derived-from/cv-term/@terminology
Cellosaurus/cell-line-list/cell-line/disease-list
Cellosaurus/cell-line-list/cell-line/disease-list/cv-term
Cellosaurus/cell-line-list/cell-line/disease-list/cv-term/@accession
Cellosaurus/cell-line-list/cell-line/disease-list/cv-term/@terminology
Cellosaurus/cell-line-list/cell-line/name-list
Cellosaurus/cell-line-list/cell-line/name-list/name
Cellosaurus/cell-line-list/cell-line/name-list/name/@type
Cellosaurus/cell-line-list/cell-line/reference-list
Cellosaurus/cell-line-list/cell-line/reference-list/reference
Cellosaurus/cell-line-list/cell-line/reference-list/reference/@resource-internal-ref
Cellosaurus/cell-line-list/cell-line/same-origin-as
Cellosaurus/cell-line-list/cell-line/same-origin-as/cv-term
Cellosaurus/cell-line-list/cell-line/same-origin-as/cv-term/@accession
Cellosaurus/cell-line-list/cell-line/same-origin-as/cv-term/@terminology
Cellosaurus/cell-line-list/cell-line/@sex
Cellosaurus/cell-line-list/cell-line/species-list
Cellosaurus/cell-line-list/cell-line/species-list/cv-term
Cellosaurus/cell-line-list/cell-line/species-list/cv-term/@accession
Cellosaurus/cell-line-list/cell-line/species-list/cv-term/@terminology
Cellosaurus/cell-line-list/cell-line/str-list
Cellosaurus/cell-line-list/cell-line/str-list/marker-list
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/@conflict
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/@id
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data/alleles
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data/source-list
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data/source-list/reference-list
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data/source-list/reference-list/reference
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data/source-list/reference-list/reference/@resource-internal-ref
Cellosaurus/cell-line-list/cell-line/str-list/marker-list/marker/marker-data-list/marker-data/source-list/source
Cellosaurus/cell-line-list/cell-line/str-list/source-list
Cellosaurus/cell-line-list/cell-line/str-list/source-list/reference-list
Cellosaurus/cell-line-list/cell-line/str-list/source-list/reference-list/reference
Cellosaurus/cell-line-list/cell-line/str-list/source-list/reference-list/reference/@resource-internal-ref

Cellosaurus/cell-line-list/cell-line/web-page-list
Cellosaurus/cell-line-list/cell-line/web-page-list/url
Cellosaurus/cell-line-list/cell-line/xref-list
Cellosaurus/cell-line-list/cell-line/xref-list/xref
Cellosaurus/cell-line-list/cell-line/xref-list/xref/@accession
Cellosaurus/cell-line-list/cell-line/xref-list/xref/@category
Cellosaurus/cell-line-list/cell-line/xref-list/xref/@database
Cellosaurus/cell-line-list/cell-line/xref-list/xref/property-list
Cellosaurus/cell-line-list/cell-line/xref-list/xref/property-list/property
Cellosaurus/cell-line-list/cell-line/xref-list/xref/property-list/property/@name
Cellosaurus/cell-line-list/cell-line/xref-list/xref/property-list/property/@value
Cellosaurus/cell-line-list/cell-line/xref-list/xref/url
Cellosaurus/copyright
Cellosaurus/header
Cellosaurus/header/description
Cellosaurus/header/release
Cellosaurus/header/release/@nb-cell-lines
Cellosaurus/header/release/@nb-publications
Cellosaurus/header/release/@updated
Cellosaurus/header/release/@version
Cellosaurus/header/terminology-list
Cellosaurus/header/terminology-list/terminology
Cellosaurus/header/terminology-list/terminology/@description
Cellosaurus/header/terminology-list/terminology/@name
Cellosaurus/header/terminology-list/terminology/@source
Cellosaurus/header/terminology-list/terminology/url
Cellosaurus/header/terminology-name
Cellosaurus/publication-list
Cellosaurus/publication-list/publication
Cellosaurus/publication-list/publication/author-list
Cellosaurus/publication-list/publication/author-list/person
Cellosaurus/publication-list/publication/author-list/person/@name
Cellosaurus/publication-list/publication/@city
Cellosaurus/publication-list/publication/@country
Cellosaurus/publication-list/publication/@date
Cellosaurus/publication-list/publication/editor-list
Cellosaurus/publication-list/publication/editor-list/person
Cellosaurus/publication-list/publication/editor-list/person/@name
Cellosaurus/publication-list/publication/@firstpage
Cellosaurus/publication-list/publication/@institute
Cellosaurus/publication-list/publication/@internal-id
Cellosaurus/publication-list/publication/@lastpage
Cellosaurus/publication-list/publication/@name
Cellosaurus/publication-list/publication/@publisher
Cellosaurus/publication-list/publication/title
Cellosaurus/publication-list/publication/@type
Cellosaurus/publication-list/publication/@volume
Cellosaurus/publication-list/publication/xref-list
Cellosaurus/publication-list/publication/xref-list/xref
Cellosaurus/publication-list/publication/xref-list/xref/@accession
Cellosaurus/publication-list/publication/xref-list/xref/@category
Cellosaurus/publication-list/publication/xref-list/xref/@database
Cellosaurus/publication-list/publication/xref-list/xref/url

cellosaurus_xpath.png