organism_verification.Rmd

---
title: "organismVerification"
output: html_document
---

# purpose: identify samples/variables with non-human descriptors from the dataset (dataset21and22)

# isolation source
```{r}
# values of interest:
# feces from 52 yr old caucasian male
# feces from 53 yr old caucasian female
# feces of 51 yr old caucasian female with stage I colorectal cancer	
# infant under 1 year of age, breastfeeding, had prelonged diarrhea

# ^ circle back and add ages for these values
# other than that, no values of interest with non-human descriptors 
```


# sample type
```{r}
View(table(dataset21and22$`sample type`))

"
values of interest:
whole organism
cell culture
pure culture
Cell culture
Bacterial culture
Culture
mixed culture
culture
Pure culture
cultured bacterial isolate
single bacterium
Microbe isolate
Pure cell culture
soil # remove this one for sure
SINGLE STRAIN

"
```

# investigation type
```{r}
View(table(dataset21and22$`investigation type`))

# nothing of interest
```



# isolate
```{r}
" values of interest:
Clostridioides difficile	
Salmonella wangata
Enterobacteriaceae
"

```

# strain
```{r}
"
values of interest:
Vancomycin resistant Enterococcus faecium
Salmonella enterica subsp. enterica serovar Enteritidis
"
```

# serovar
```{r}
"
values of interest:
Typhimurium

"

# this one is a headache. circle back to it after you've removed samples based on other variables
# same with sub species 
```

# lab host
```{r}
"
Sus scrofa (gnotobiotic piglets)
"
```

```{r}

```





# common name
```{r}
"
many descriptors here for uncultured bacteria. 
check with Jess for how to proceed with these samples
if the sample is from an identified species, should it be excluded? 
same with `Inferred taxonomy`, `genus`, and `species`
"
```

# organism modifier note
```{r}
"
vancomycin resistant enterococci
"

```



# component organism
```{r}
# Aeromonas caviae
```